I think it's best to rank them by tiers. You just can't compare different generations with different rules.
Super Bowl Era
Tier One- Tom Brady, John Elway, Joe Montana
Tier Two- Troy Aikman, Terry Bradshaw, Peyton Manning, Dan Marino, Roger Staubach, Steve Young
Tier Three- Dan Fouts, Fran Tarkenton, Jim Kelly, Donovan McNabb, Warren Moon, Ken Stabler
Tier Four- Ken Anderson, Drew Brees, Brett Favre, Kurt Warner
I know I left out Joe Namath. He sucks, and he didn't play well in the "the most important game ever." And Favre is lucky to get fourth tier, if you base a quarterback on the percentages he gives the team to win a game.