I still believe you have to separate guys by era. But that's just me. There's no question Brady is the greatest in the salary cap era, as much as I dislike him. Maybe it'll come out one day that he's been using performance enhancing drugs for years or something.
For me, the era before this, Montana was the greatest. He won Super Bowls in every way it's possible - blowouts and close games won at the end. He was perfect and never threw a pick (Lewis Billups must have kicked himself until the day he died about that).
Some people say look at the teams Montana had and how easy it was to maintain them. That's true, but I also think the level of competition isn't the same these days, and QBs have it so easy. I mean Brady cries to the ref whenever a defensive player looks at him the wrong way, and usually gets a flag. So I think these things offset.
Maybe you tend to go with the guy you grew up watching. People from the generation before mine will often say Jonny U is the greatest.
Ask yourself this. Your life is on the line in the biggest game, your team has the ball with 2 minutes left, which QB do you choose? I'd choose Joe Cool. He was perfect in the big games and that can never be changed.