so i got meyer sheriff and he told me cooke and eddie are the leaders of the gang powders, can i take back the prison by killing them? it ain't a quest so i'm not sure

Not sure, I cleared out the prison early on in the game, and now, over 20hrs later, it remains vacant. So I don't think its an unmarked quest or anything, but others may know better. I do beleive that their are some ending slides related to the NCRCF, but I've been puting off the ending so I'm not sure. :shrug:

There is actually quest where you can help NCR to retake prison: http://fallout.wikia.com/wiki/I_Fought_the_Law#Notes

cooke isnt even in ther prison. nhes way far away up north.

There is an event you can get that lets you help the ncr retake the prison but its nearly impossible to stumble apon it as you have to do some quests FOR the powder mgangers first before you can trigger it and franlly powder gangers are just sooo fun to pop.