I love me some Tom Brady but he's still the second best QB in the league. Manning calls his own plays, has made a slew of receivers look like All-Pros, and won without the benefit of an outstanding defense.
Given the choice in a complete vacuum, "Who would you want to QB your team for one game to win a championship?" I would probably have to take Manning, though the choice is very, very close and difficult.
I still say though, that asked that question out of the vacuum in reference to how they are playing this year, I still take Brady second after Manning over some of the QBs having career years in the league. You just can't replace great experience