I take Brady, and its not really close.
I think, although it is Monday, that Brady hasn't won a Super Bowl with the help of Moss. I believe all his other SB's were won with their best WR being Deion Branch and a RB core of a bunch of no names. I think while Manning is a great QB, puts up great numbers, has great pocket awareness, but I think Brady has that "it" quality. He used to be a tough as nails QB, who knew what had to happen in order to get the job done. He always reminded me of a QB who took it one step at a time.
FWIW I take the old Brady, the pre-uber celebrity QB.