I voted Brady over Manning, as much as I hated to. The reason why is that Brady, right now has better stats in three of the most important categories - Wins, Playoff Wins and Superbowl Wins. By the end of the season, I think that Manning will have a belt full of new records, which will increase his stature in the NFL QB benchmark world. However, until he wins a few more playoff games and another Superbowl, its hard for me to rank him over Brady in the modern QB era.
As for the "Brady wouldn't have made it as a QB in earlier years" argument... who is to say? With the ever changing rules of the NFL its just too hard to theoretically compare one QB to another of a different generation. A lot of the rules today do help the QB, but some rules, like the old force out rule, could be considered an advantage to some of the older QBs. You have to take the man in his context of when he played, how he played, what he did, and what he accomplished with what he had.
For the best to accomplish what they did with what they had, its hard not to argue Elway. Otto Graham did a ton with what he had on the Browns. Bart Starr and Montana were surrounded by greatness, but accomplished their own feats with convincing style.
One of my favorite articles of all time is the one where it compares Elway to Montana and ranks Elway as the better QB for having done so much with such bad teams.
Also - Unitas.