I vote vita because it has Uncharted and I'm a huge fan of the series. Plus if we look at PSP it had 2 God of Wars games, GTA and some other great titles, so most likely the Vita will get those eventually as well.
3DS is more of Nintendo's "gimmick-marketing" imo, they put 3D with no glasses and seem to make that the main selling point, personally that doesn't do it for me. But if you think its really neat then maybe the 3DS is your cup of tea. (Just a note, I'm not trying to flame 3DS or owners of it, its just not my preference but if you like it then I'm glad for you

I would advise you to hold off, at least a little while, if you decide on the Vita because it's sales haven't been very strong. I get the feeling it will receive a price drop much like the 3DS did last year.