Mike Shea had a great idea for creating tougher versions of monsters: double it's hit points, add +2 to its attack rolls, damage, and DCs, and give it one extra attack as part of its attacks action. This will make it about twice its base CR. You can also increase its size by one step if you want it to look bigger and badder.
EDIT: I reread this and realized you're asking for a tool. I'm afraid I can't be of any help there. Maybe just put all of the above into the DDB homebrew thing? When I do this in person, I usually jot all this down on a sticky note and put it on the monsters page in the MM.
The easiest tool to use for increasing CR is to use the Monster Manual Expanded and Monster Manual Expanded II. You can pick it up from the dmsguild.com. You'll notice that in 5E, WotC has been neglectful of content past level 12 for parties. From 0-12 there are 86 pages in D&D Beyond, for 13 to 30 there are 12 pages. Those two expanded monster manuals are very good and useful to fill up the lack of content for higher level play. It makes it easier than doing the calcs in the DMG or if you need a quick monster.
I have more or less abandoned CR's with the exception for identifying when encounters are going to be vastly beyond the party's capabilities (if the encounter is worth double the Deadly XP level, it's too tough). The difficulty suggested simple doesn't compare to what a party is capable of doing, in part because the moment one or two creatures go down, the encounter difficulty drops massively. I find it deeply tedious to have to roll initiative for a bunch of creatures that I know are going to die within one round of combat, and there's little in it for the players.
My experience with the Encounter Builder tool is:
All encounters of Medium difficulty and below should be considered Trivial. They will rarely last more than 2 rounds at most, and are usually ended by a single spell. Example: 5 x Level 8 characters vs. 2 Trolls is considered Medium. With only 84 hit points, I would expect one troll to die before taking its turn, and the second to be mopped up halfway through the second turn of combat.
Encounters of Hard difficulty should be considered Easy, and unless they have a hard hitting breath weapon to unleash in the first turn, will probably not cause any significant challenge. They may last as many as 3-4 turns of combat. If the party are fresh and prepared to blow what we'd call 'Cooldowns' in the MMORPG world, then the party will have done sufficient damage in the first turn of combat to have reduced the enemy threats to a Medium or below encounter, and probably just spend a couple of turns using Cantrips and basic attacks to finish the enemy off. Example: 5 x Level 8 characters vs. 1 Green Slaad and 1 Red Slaad. If the Red Slaad lives long enough to take a turn and manages to hit with all three attacks, it will inflict just 22 damage on average. It is a negligible challenge. Hitting with all 3 attacks, the Green Slaad will deal only 33 damage. Together they'll manage an average 55 damage if they hit with everything against a target with no defences.
Encounters that just push over into Deadly difficulty should be considered the standard - Medium. They will typically offer 4-5 turns of combat, allowing the characters to make significant choices about what abilities to use. Example:A Mage riding a Winter Wolf, supported by a Young Black Dragon is Deadly for our 5 level 8 characters. The encounter offers some choices about targetting. Of course, the mage will almost certainly be dead before the end of the first turn unless he starts with Greater Invisibility up. There are many ways to make this encounter trivial difficulty of course - Banishment will do it just fine.
A generally good rule is that if an individual creature's CR is double that of the average party level, then the creature will likely have access to spells or abilities that the party cannot handle - a level 8 party cannot effectively cope with a CR17 Death Knight's Hellfire Orb, for instance.
CR does work for low to mid level as long as you keep the party engaged with combat and watch the amount of magic items you give the party. If you use the loot tables from the 5E modules, you might as well be doing acid than playing D&D as the DM. My party is going to see their first +2 magic item with no strings attached soon and they'll be level 16. CR does become a problem in the mid to late teens, you will be running hard to deadly encounters to keep the party engaged. Also, don't forget to have mobs flee - and then add them to later encounters or the boss encounter if you feel its a weak encounter.
Also, look at your players abilities, build encounters that fight their strengths. My party was melee heavy and used it to kill their prey, so I created some acid trolls based off the venom troll (party paladin is yuan-ti), and it was one of the harder encounters for them because every time they attacked, acid blood covered them and they took AE damage. Did I mention AE damage? Use AE damage attacks on higher level parties to keep them under the gun. It pressures the healer and there's a good chance one or two of the clothies will go down.
CR isn't necessarily the problem, its the monsters that 5E put out, they are particularly weak for special abilities. Homebrew in when you need something strong. Use beasts with legendary resistance or counterspell to deal with caster heavy parties. If the party has a paladin, then use monsters/spells that attack intelligence (its the dump stat for almost everyone). If you have to, create monsters or spells with abilities that attack intelligence. I've got a monster family that uses spell shot weapons that fires mind sliver at 5th or 11th level - it doesn't do a tremendous amount of damage but if they fail their int saving throw, they lose 1d4 on their next saving throw and take normal cantrip damage. You can use it as a way of softening up parties that have really strong saves so spell effects come in. If you see players taking bad risks because they feel invulnerable (again its the paladin in 5E, that save aura was a really bad call), and I've seen it in parties, you have to think of a way to make the world scary again or you'll start losing players to boredom.
For the mage on the Young Black Dragon, did the mage have Counterspell up to stop banishment? Start the mage off with Mage Armor (AC 15) then if he does get hit (Shield) for AC 20. Why have the mage show himself? Why not have the winter wolf or dragon start out with greater invisibility and lure the party to the helpless mage and when they get in a nice tight cluster, HIHI folks here's your dragon breath with a winter wolf chaser and here's your fireball from the mage. Or better yet why not use a young dragon with a cone attack rather than line? Average AE damage is 42 (green dragon breath) + 24 (fireball) + 18 (winter wolf breath). If a character fails they take 84 damage on save its 42 damage. If the party screws up their positioning or initiative rolls gets the winter wolf early before it can be eliminated, there is a high likelihood of one or two characters going down in the opening. And yes the party can AE as well but will take one counterspell, which will shock them if you don't use it. Hell, remove cone of cold and replace it with wall of fire, read it, its ridiculously nasty in 5E. They get one save and if they enter it (get pushed) they take full damage no save, its hella lethal.
Mike Shea had a great idea for creating tougher versions of monsters: double it's hit points, add +2 to its attack rolls, damage, and DCs, and give it one extra attack as part of its attacks action. This will make it about twice its base CR. You can also increase its size by one step if you want it to look bigger and badder.
EDIT: I reread this and realized you're asking for a tool. I'm afraid I can't be of any help there. Maybe just put all of the above into the DDB homebrew thing? When I do this in person, I usually jot all this down on a sticky note and put it on the monsters page in the MM.
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The easiest tool to use for increasing CR is to use the Monster Manual Expanded and Monster Manual Expanded II. You can pick it up from the dmsguild.com. You'll notice that in 5E, WotC has been neglectful of content past level 12 for parties. From 0-12 there are 86 pages in D&D Beyond, for 13 to 30 there are 12 pages. Those two expanded monster manuals are very good and useful to fill up the lack of content for higher level play. It makes it easier than doing the calcs in the DMG or if you need a quick monster.
I have more or less abandoned CR's with the exception for identifying when encounters are going to be vastly beyond the party's capabilities (if the encounter is worth double the Deadly XP level, it's too tough). The difficulty suggested simple doesn't compare to what a party is capable of doing, in part because the moment one or two creatures go down, the encounter difficulty drops massively. I find it deeply tedious to have to roll initiative for a bunch of creatures that I know are going to die within one round of combat, and there's little in it for the players.
My experience with the Encounter Builder tool is:
All encounters of Medium difficulty and below should be considered Trivial. They will rarely last more than 2 rounds at most, and are usually ended by a single spell.
Example: 5 x Level 8 characters vs. 2 Trolls is considered Medium. With only 84 hit points, I would expect one troll to die before taking its turn, and the second to be mopped up halfway through the second turn of combat.
Encounters of Hard difficulty should be considered Easy, and unless they have a hard hitting breath weapon to unleash in the first turn, will probably not cause any significant challenge. They may last as many as 3-4 turns of combat. If the party are fresh and prepared to blow what we'd call 'Cooldowns' in the MMORPG world, then the party will have done sufficient damage in the first turn of combat to have reduced the enemy threats to a Medium or below encounter, and probably just spend a couple of turns using Cantrips and basic attacks to finish the enemy off.
Example: 5 x Level 8 characters vs. 1 Green Slaad and 1 Red Slaad. If the Red Slaad lives long enough to take a turn and manages to hit with all three attacks, it will inflict just 22 damage on average. It is a negligible challenge. Hitting with all 3 attacks, the Green Slaad will deal only 33 damage. Together they'll manage an average 55 damage if they hit with everything against a target with no defences.
Encounters that just push over into Deadly difficulty should be considered the standard - Medium. They will typically offer 4-5 turns of combat, allowing the characters to make significant choices about what abilities to use.
Example: A Mage riding a Winter Wolf, supported by a Young Black Dragon is Deadly for our 5 level 8 characters. The encounter offers some choices about targetting. Of course, the mage will almost certainly be dead before the end of the first turn unless he starts with Greater Invisibility up. There are many ways to make this encounter trivial difficulty of course - Banishment will do it just fine.
A generally good rule is that if an individual creature's CR is double that of the average party level, then the creature will likely have access to spells or abilities that the party cannot handle - a level 8 party cannot effectively cope with a CR17 Death Knight's Hellfire Orb, for instance.
CR does work for low to mid level as long as you keep the party engaged with combat and watch the amount of magic items you give the party. If you use the loot tables from the 5E modules, you might as well be doing acid than playing D&D as the DM. My party is going to see their first +2 magic item with no strings attached soon and they'll be level 16. CR does become a problem in the mid to late teens, you will be running hard to deadly encounters to keep the party engaged. Also, don't forget to have mobs flee - and then add them to later encounters or the boss encounter if you feel its a weak encounter.
Also, look at your players abilities, build encounters that fight their strengths. My party was melee heavy and used it to kill their prey, so I created some acid trolls based off the venom troll (party paladin is yuan-ti), and it was one of the harder encounters for them because every time they attacked, acid blood covered them and they took AE damage. Did I mention AE damage? Use AE damage attacks on higher level parties to keep them under the gun. It pressures the healer and there's a good chance one or two of the clothies will go down.
CR isn't necessarily the problem, its the monsters that 5E put out, they are particularly weak for special abilities. Homebrew in when you need something strong. Use beasts with legendary resistance or counterspell to deal with caster heavy parties. If the party has a paladin, then use monsters/spells that attack intelligence (its the dump stat for almost everyone). If you have to, create monsters or spells with abilities that attack intelligence. I've got a monster family that uses spell shot weapons that fires mind sliver at 5th or 11th level - it doesn't do a tremendous amount of damage but if they fail their int saving throw, they lose 1d4 on their next saving throw and take normal cantrip damage. You can use it as a way of softening up parties that have really strong saves so spell effects come in. If you see players taking bad risks because they feel invulnerable (again its the paladin in 5E, that save aura was a really bad call), and I've seen it in parties, you have to think of a way to make the world scary again or you'll start losing players to boredom.
For the mage on the Young Black Dragon, did the mage have Counterspell up to stop banishment? Start the mage off with Mage Armor (AC 15) then if he does get hit (Shield) for AC 20. Why have the mage show himself? Why not have the winter wolf or dragon start out with greater invisibility and lure the party to the helpless mage and when they get in a nice tight cluster, HIHI folks here's your dragon breath with a winter wolf chaser and here's your fireball from the mage. Or better yet why not use a young dragon with a cone attack rather than line? Average AE damage is 42 (green dragon breath) + 24 (fireball) + 18 (winter wolf breath). If a character fails they take 84 damage on save its 42 damage. If the party screws up their positioning or initiative rolls gets the winter wolf early before it can be eliminated, there is a high likelihood of one or two characters going down in the opening. And yes the party can AE as well but will take one counterspell, which will shock them if you don't use it. Hell, remove cone of cold and replace it with wall of fire, read it, its ridiculously nasty in 5E. They get one save and if they enter it (get pushed) they take full damage no save, its hella lethal.
https://1-dot-encounter-planner.appspot.com/quick-monster-stats.html
https://********/crcalculator.html#0,13,1,3,false,Medium,1,10,false,0,false,0,
https://tetra-cube.com/dnd/dnd-statblock.html
All of these website used separate or in conjunction are great for DMs wanting to make or adjust monsters .