How do you capture Thunderus, I've got a Crobat Lv 52 Air Cutter ..

Use mean look stop it from fleeing, use endeavor while kyurem is weak to lower thunderus' hp and give it a status ailment (you don't have a Pokemon that can do that so I suggest you to get one).
Then throw a lot of ultra balls or dusk balls during night.
That should work. You can also use a master ball. :P

I would use mean look (since mean look keeps it from running away) and since mean look only works when crobat is battling him then I would just use him with poison fang until his health is low . Then Capture

Dude for starters your Pokemon levels are way to high try to get a crobat on level 43 with mean look also have lots of ultra balls and great balls.

To catch thunderus have your starter a Pokemon that can use mean look or has the ability shadow tag or arena trap and have a Pokemon that can use a move that paralyzes or makes thunderus fall asleep then have a Pokemon that can use false swipe and have ultra balls and dusk balls if it is night time use dusk balls if daytime use ultra balls or use your master ball