I'm running a homebrew campaign called The Nine Seas, and in each sea there's meant to be one Dreaded Captain, essentially the equivalent of the pirate lords from Pirates of the Caribbean. I've already got two of the nine nailed down, a captain who commands a dragon flesh golem, and one who managed to turn himself into a were-gator. Any ideas on what I should do for the other Dreaded Captains?

First question: do you actually need to decide now? If you don't, you can toss around ideas in your head for a while.

Second question: are you doing any kind of tactical ship-to-ship combat? (If you are, then you have the whole realm of abilities for that part of combat to play with.)

Anyway:

• Weather control
• Can't die through normal means
• Summons minions, possibly undead
• Cold powers; their ship is carved out of an iceberg
• Whirlpools
• Split into multiple bodies

I need one as soon as possible. i had to build the commonly found enemies of the northwest sea, but didn't get to the dreaded captain in time. The captain of each sea is encountered if A: the part actively seeks them out or B: I roll a nat 20 on my random encounter. as for your other question, yes tactical naval combat has been a thing, one of my players is an aaracokra, another a druid who turns into a giant octopus, which means sea battles get very interesting.

I have a Pirate captain in my campaign right now called The Dread Pirate Bloberts who is an ooblex impersonating an entire Pirate crew. Basically the entire ship is being run by the body doubles it creates while the ooblex "core" sits in the hull of the ship. My party is in the process of hunting it down, and I'm planning to do some impostor/shape-shifting stuff and creepy clone encounters. Something to consider!

Quote from Gaberielstickslapper >>

I need one as soon as possible. i had to build the commonly found enemies of the northwest sea, but didn't get to the dreaded captain in time. The captain of each sea is encountered if A: the part actively seeks them out or B: I roll a nat 20 on my random encounter. as for your other question, yes tactical naval combat has been a thing, one of my players is an aaracokra, another a druid who turns into a giant octopus, which means sea battles get very interesting.

 

 I think you might want to reconsider the party stumbling upon a very important NPC just because you got a specific number on a die. That just doesn't seem like a good idea.

The dreaded captains aren't wildly necessary to the campaign, they're more just a high priority side quest. defeating all nine will make the bbeg fight easier. also, the part can search out the captains if that's what they want to do, the 20 on the encounter roll is to see if the dreaded captain finds them.

First, I’d agree with Maruntoryx that you shouldn’t leave it to chance. You want these fights to be interesting and memorable. That means choosing the most dramatic time for them to make an entrance, and choosing a level appropriate challenge. If it’s random, they could accidentally bump into someone much too strong, or too weak, and do it when there’s no stakes. 
Yes, it might be more “realistic” but don’t let a search for realism get in the way of a story. 

As for ideas for captains, I’m not sure the level you were going for, but: A lich, a beholder, a dragon in humanoid form, a death knight, an aboleth, a hag, a cultist heirophant. Really any intelligent creature could be.

I recommend having one captain who's entirely mundane.  Just a human/elf/dwarf/whatever with no magic, but they have a ship that's faster and more heavily armed than anyone else's.  If gunpowder isn't normally a thing in the world, they have cannons.  If it is, their cannons are more accurate, more powerful, and longer ranged than anyone else's.

One of the Captains is very effective at espionage. They have informants everywhere there is no secret kept by the party. They know their plans of attack from spies and divination. The Captain has a counter for Every move the party makes. Make them a divination Wizard, or the first mate is.

Perhaps the Captain is a Fathomless warlock and can shoot her Eldritch blast a very long way to engage the party for several rounds before they can attack, possibly even slowing the ship down as well.

The ship is a submarine and the party can never find it until it attacks them, with surprise. Torpedoes from the artificer, maybe? Summons from the wizard or a ritual or maybe just blowing a horn underwater to summon allies.

First, a silly idea: a storm giant that can breathe underwater who walks along the ocean floor and wears a boat as a hat.

Second, a cool idea: a crew of sorcerers, wizards, warlocks, etc. in small sailboat with a hatch in the middle that leads to a demiplane interior. You can only see two or three pirates on the outside, but the remaining crew are in the demiplane.

How about a merfolk captain whose ship sails under the waves? A storm giant captain whose enormous ship is the source of all the storms on one of the 9 seas? 

Here's some ideas for Dread Captains:

Ghost or Undead Captain who sails the same ship that sank and drowned them. They only manifest on nights with a new moon and emerge dramatically from under the waves. They are unkillable while in darkness but can be weakened & destroyed while in bright light. They have various wind-magic, and water-magic abilities which they can use to extinguish flames / light or to try to drown their enemies (preventing the enemy from casting spells) even above land. 

The Flying Dutchman, whose ship can literally fly and can land on enemy ships in an attempt to capsize / smash that ship. The captain & crew can jumps down from above with ropes to and have cools swinging / rope based abilities to increase their movement or deal AoE damage while swinging across an enemy ship's deck on the ropes. 

The King/Queen of the Sea - a merefolk Pirate Captain whose "ship" is a giant dragon turtle, with a crew of Sirens, merefolk and Harpies that try to charm enemies into jumping off of their ship into the ocean where the dragon turtle or a swarm of sharks / dolphins attack & kill them.

The Invisible Ship - a Pirate Captain with a talent for illusion magic, nobody knows what they actually look like because they are always hidden under an illusion, their ship can turn invisible, and the captain themselves can conjure illusory duplicates, turn themselves / allies invisible, and create illusory monsters to scare their enemies into surrendering their loot. This captain doesn't particularly want to fight, but more tries to convince their opponents to pay up to be left alone.

Heart of the Storm - A pirate captain turned insane after surviving being hit by lighting. They are obsessed with lightning and storms getting a rush whenever they are struck by natural lightning. They chase storms and channel lightning through themselves to strike and destroy other ships purely from insane worship of storm gods.

Shark Hunter - A big burly Barbarian-type character known for wrestling and killing sharks in hand-to-hand combat. They wear necklaces of shark-teeth and shark-skin leather clothing. They and the crew are all big and burly with some unique abilities / weapons related to mechanical shark-jaws traps, harpoons, shark tooth bows & arrows. 

Yuri - A servant of an Aboleth that has mind controlled their entire crew to believe they are just a normal guy despite being covered in slime and having weird tentacles. They have various mind-control abilities.