Both are brilliant, i'm getting sick of all the hate for mw2 though, but i guess there are enough x360 mw2 fanboys out there to compensate.
MW2 = short story that doesn't explain itself well but intense and fun, awesome co-op spec-ops mode, fantastic mp.
Uncharted 2 = Good story, great cut-scenes and decent length, amazing graphics, super polished, mp is lacking and no offline co-op.
It's a really tough one, i honestly expect game sites decisions to be split between these two...
For me personally though i say Uncharted 2 as i don't play much multiplayer on console's, and i still honestly believe no fps has yet to top counter strike on multiplayer.
boom headshot =)