Okay to put it simply it is like comparing apples and oranges...until now. Lets make it this situation:
Peyton Manning has the WR's that go by the names of Reche Caldwell, Troy Brown, Jabar Gaffney, Doug Gabriel, Chad Jackson, Kelvin Kight, Benjamin Watson, Daniel Graham, and David Thomas.
Now i mean no disrespect for the Patriots Receivers, and I love them all, but lets faces it. Manning with this set, would probably barely be able to throw 3,000 yards. brady managed to get 3,500 with these. When i think about it more, Manning plays a style of offense, where he has one or two very dominate receivers, he throws to on pretty much any play. So my guess is that Manning would not have the ability to spread the ball around this many receivers. It is amazing what Brady was able to do with these players.
now Brady has Marvin Harrison, Reggie Wayne, and Brandon Stokely. Now, I don't think that the Patriots or Tom Brady like playing with just a few receivers, and like to spread the ball around, but i bet that Tom could get along fine with this set or wide outs. I could see Brady throwing in the middle-upper four thousands, while still playing the run. The deep threat would prevent safties from playing up, and a player like Marony would prosper, being able to make it into the open.
So my opinion is that the only reason manning is this good is because of the talent around him, and that if he were to lose his great receivers he would be no where as close to as good he is right now. I think that this is the first year we might actually be able to compare them fairly.
But all this offensive line talk, the Colts are only making it better by adding the amazing talent of Tony Ugoh on their line, drafting him a round early.
Edit: But just to make the point, both are the two best playing now, and I think both of them are hall of famers.