First define "fair" and define "rate." Fair and rate and not mutually exclusive. Any rating is going to result in a ranked list, correct? So the best way if you really wanted, to be empirical, would be to develop an index (like QB rating or QBR) based on variables that everyone considers "fair" (ie, they're relevant... wins matter but height doesn't and isn't a fair varuable so Doug Flutie doesn't lose points!). Then you weight certain variables... Super Bowls are weighted more than regular season wins. It gets to be cumbersome, complex and still arguably subjective. I also think the QB Rating and QBR attempts in some way to do this...
All that aside, I look at it this way.... who would I want starting for my team in one Super Bowl in his prime. Or whose career would I take to enjoy for its totality and his team's success and the answer is clear... Tom Brady hands down. Although in my lifetime of being a fan includes some of the greats, Brady is the guy. I believe in cerebral QBs and I'd take Montana second, Manning third. You want to standardize or normal stats to compare guys across eras and schemes... look at TD to INT ratios. A high TD total is meaningless if you're comparing this era to prior eras given the propensity to pass more. But the TD:INT ratio, in my mind, explains decision making and brains and not turning the ball over is certainly a predictive variable for wins. Brady's ratio is 2.69:1. Manning's 2.17:1. Montana's 1.96:1 and Marino's who I think is the most overrated QB of my lifetime was a dismal 1.66:1.
Any by the way Montana had some guy name Rice he threw too and Manning some dudes named Harrison and Wayne. Brady's cast of characters is a litany of number 2 QBs.
The problem here is, people have so much distain, like I used to for Brady, that they refuse to look at the guy objectively, instead trying to cut him down with stupid arguments like "He didn't kick the SB winning FGs." SO myopic.