Brady and Manning are the best in the game now and both HOF bound. With that said look at what Brady did in previous years without a top WR corp. This year was the first year that Manning didn't have his normal stable of receivers and he struggled. I think both qb's can do great when they have a good situation (good WR's, time to throw, ect..) I think what makes Brady a little better is how he does when he's getting pressured, knocked down, end of game situations, ect... Brady is compared to 'joe cool' for a reason, it's because of his temperament and record when times are tough and the games on the line. Manning tends to break down a little when things aren't going well, while Brady keeps going.
Just my $.02