For my money the Greatest QB in the Super Bowl era is Joe Montana, 4-0 in Super Bowls and NEVER threw a SB INT. The #2 QB, that I've seen play, is Johnny Unitas, the master of the 2 minute drill.
Peyton as a QB craftsman is one of the best of all-time, but his brother, Eli, has more SB wins. (As a younger brother I hope that doesn't change.)
One other factor in my best of all time: If I bet against that player specifically because they were playing in a BIG game and handicapped a CHOKE, then they can't make my best of all-time, e.g. Marino, Favre, & P. Manning.