So... I'm a DM, I'm running a homemade dungeon where the villain is a necromancer. Built him as a 7th level Eladrin Wizard (Necromancy) and his spell list includes the spells Blight and Counterspell. The party contains a Chronourgy Mage (bugbear) who will most likely try to Chronal Shift the Blight spell when the Necromancer uses it. Can the Necromancer use Counterspell on the chronal shift?

I am assuming you mean allowing the affected character to reroll their saving throw. In this case no you cannot counterspell chronal shift as it is an ability. Counterspell's trigger for casting is when you see another creature casting a spell within 60ft of you so counterspell would not work on this. However if the wizard tried to counterspell the spell or cast silvery barbs then you obviously could. Hope this helps

Typical ways to stop counterspell:

1) Sorcerer using Subtle spell - nothing to see or hear.

2) Darkness or other ways to block light.

3) Wait till they used their reaction or better yet get them to use it on a cantrip.

4) Be 61 ft away from the casters.

 Counterspell can only be cast in response to a spell cast, not when using a feature such as Chronal Shift. 

Quote from KyrneGnomeBarbarian >>

So... I'm a DM, I'm running a homemade dungeon where the villain is a necromancer. Built him as a 7th level Eladrin Wizard (Necromancy) and his spell list includes the spells Blight and Counterspell. The party contains a Chronourgy Mage (bugbear) who will most likely try to Chronal Shift the Blight spell when the Necromancer uses it. Can the Necromancer use Counterspell on the chronal shift?

The text is clear on this. The reaction trigger for Counterspell is "which you take when you see a creature within 60 feet of you casting a spell". Chronal Shift is not a spell, so Counterspell cannot trigger off of it.

My logic was that the chronourge is obviously doing something magical to MANIPULATE TIME ITSELF and so it should be Counterspell-able but I guess this works.

Quote from KyrneGnomeBarbarian >>

My logic was that the chronourge is obviously doing something magical to MANIPULATE TIME ITSELF and so it should be Counterspell-able but I guess this works.

 
Counterspell doesn't counter magic. It counters spells. It is something that stops a specific use of magic, not just any use of magic. It's the same reason you cannot counterspell a dragon's breath attack even though it's a use of magic. 

Chronal Shift is magical, but it's not a spell. Counterspell only applies to spells.

What you are seeking is Antimagic Field. This will stop Chronal Shift if the wizard is in that area of effect.

Too high level.

You're the DM. So, no it's not. If you want something to have it, it has it. Levels are a player thing. You're not a player. You're the DM. You are the game itself. If it is relevant for antimagic field (be it spell, a room or lair effect, a monster ability, whatever) then you can have it there. 

Fair point.