I'm not sure who is better (both are probably top 5 all-time), but I think that I would choose Tom Brady. He seems to be a little more calm in the pocket, and I think he's the tougher guy. Plus, he's won more Super Bowls. Brady finally has some talent at WR, but he still doesn't have the weapons Manning does.
Marvin Harrison, Reggie Wayne, Addai, and Dallas Clark are greater than Randy Moss, Wes Welker, Ben Watson, Maroney. If both players had been in each others shoes at the start of their careers, I have a feeling the Brady would have done a little better.
Bottom line is, I think Tom Brady has a special intangible quality that makes him more of a winner.