I think Brady will win in a landslide.
Still, Vick has averaged more yards of total offense per game (306.2) than Brady (255.6), is averaging almost as many passing yards per game as Brady (250.5 vs. 254.4) and is averaging more passing yards per attempt (8.4 vs. 7.9). Coming into this week's games, Vick had 28 total TDs to Brady's 32, despite playing in 2.5 fewer games. (Also, keep in mind that some of the "per game" stats are slanted against Vick, because he missed a couple of halfs during the season, once due to being the backup QB and relieving Kolb, and once due to injury).
So, it's been very, very close. I can see why somebody would argue for Vick, due to him arguably having the better overall statistics (when rushing is taken into account) and because Philly was seen as being in a rebuilding year, and is now looking like a contender.