Ok I said I'd offer more analysis after a chance to digest the list
Keep in mind a few things. Players played 12 games till 1960 and 14 games till 1978
That said the statistics for QBs have stayed fairly similar since about 1960.
Therefore if you're in the "You can't compare across eras" camp then Otto Graham can't be compared to Tom Brady or Montana, because his era was 1946-55 and don't even think of HOFer Benny Friedman. The man is to the pass what Thomas Jefferson was to democracy, as in they weren't sure it would work. I got very confused looking at his stats from 1927 to 1931 because I couldn't figure out how he had about 50 passing TDs without any passing yards or attempts. I eventually came to the conclusion that nobody recorded the stat at that time.
Other than that you can compare lots of QBs reasonably fairly.
For example in 1961 Johnny Unitas had 420 pass attempts (when they only played 14 games). There are Qbs that routinely throw quite a bit more now such as Marino, Brady, Mannings, but keep in mind Rothlisburger threw for less than 300 attempts his first two years in the league and it is routine for QBs to have less than 400 attempts. It's more the exception, but it happens a lot.
Now for some observations.
The undisputed #1 winner is Otto Graham (yes I remember what I just said. hold on). The man played in 11 championship games in 10 seasons (you read that right), and won 7. His rookie year he won a title with the AAFC Browns and in pro basketball with the Rochester Royals. The knock against him is that this was when there were only a handful of teams in the league instead of 32. When Brady wins a Super Bowl it means he beats almost 3 times as many teams, making his ring three times as valuable. That makes it 9 rings to 7.
another historical observation. In baseball history it's easy to say "Babe Ruth didn't play against minority players". It's not as easy in football because there were many leagues that had different policies regarding segregation until the NFL merger. I think Graham did play with minorities.
Anyway.
The case for Montana: undefeated in 4 Super Bowls with 3 Super Bowl MVPs. Simply Mr. Clutch. He won two Super Bowls without Jerry Rice.
The case against: Very nitpicky. He didn't have the most yards and wasn't flashiest.
The case for Dan Marino: retired with the most yards. Threw the only 5000 yard season in history and in the same year threw 48 TDs which was a record for 20 years and did it in only his 2nd year.
Case against: LOSER!
The case for Farve: Way stronger than I want to admit. Threw for the most yards ever and not done. Started more games in a row at a position with a huge target on your back than any player ever started in a row at any other position. Has more passing yards than Aikman and Steve Young combined.
Case against: nearly every fan in America that loves football wants to punch him in the face for being a big huge prima donna who was overhyped by ESPN for a decade
The case for Manning: Unbelievable stats. I mean unbelievable. Consider this. Marino threw for 4000+ yards 6 times in 17 seasons. Manning has done it 9 times in 11. Despite being thrown into the fire and starting from day 1 his 64.4% career completion rate is higher than any of these QBs other than Kurt Warner.
Case against: The Pats had his number for a decade despite playing with many pro Bowlers
The case for Brady: Stats slightly less good than Manning but 3 rings and an AFC championship ring to one. Threw 5 TDs in a quarter in the snow. Had the only unbeaten regular season among top 15 QBs. Has the highest home winning % since 1950.
The case against: Not much. He hasn't had a long career.
The case for Unitas: won a few rings. retired with 40,000 passing yards. That's 12000 more than Terry Bradshaw. That kind of production was virtually unheard of back then. It's like when Babe Ruth hit 60 home runs and the #3 guy hit 18.
Further comment
The knock on Brett is interceptions. He is the interception leader. Brady, Montana, McNabb, and Manning has rates of better than 2 TDs per INT, while Farve is 4 to 3. However it should be noted that many HOF QBs have interesting TD to INT ration
Elway was 300-226
Bradshaw was 212-210
Bart Star was 152-138
Otto G 174-135
Aikman 165-141
Staubach 153-109
Namath 173-220
F tarkenton 342-266
Dan Fouts 254-242
Bob Griese 192-172
Warren Moon 291-233
Kenny Stabler 194-222
Kerry Collins 186-179
Phil Simms 199-157
Steve mcNair 174-119
Other points of note
Randall Cunningham and Warren Moon being 38 and 24 is beyond me.
Cunningham was 2 decades ahead of his time. He went for almost 3500 passing and 1000 running in 1990.
Moon threw for 49,000 yards in the NFL right behind Elway, but when you add his CFL numbers he threw for 70,000 yards! and 435 TDs. That's more than any of the top 9 Qbs