Sure Brady is the best.
Like somebody said, it's hard to compare the guys from the 40's, 50's, 60's and even the 70's to the modern day guys. They were tackled by their head more than their legs. They got speared. You could knock their receivers down 20 yards downfield.
It's like Bonds to old timers. Put the Drysdale, Gibson or any of those flame throwers who owned the outside of the plate on the mound, take away the elbow pad and I'd bet my house he moves another 12" off the plate to become one of the best 400 homer guys.
Guys from the 40's and 50's I never saw:
Bob Waterfield
Otto Graham
Sid Luckman
Sammy Baugh
Bobby Layne
Norm Van Brocklin
Milt Plum
Guys from the 60's and 70's I did see:
Bart Starr
Y.A. Tittle
Johnny Unitas
Sonny Jurgenson
Frank Ryan
John Brodie
Roman Gabriel
Norm Snead
John Hadl
Joe Namath
Billy Kilmer
Roger Staubach
Ken Stabler
Darryl Lamonica
Give those guys the 5 yard illegal contact rule, no contact to the quarterback's head/shoulders/knees/ankles and the out-of-the-pocket rules and they might put up much better numbers than they accumulated in those days.
But any list without Fouts, Stabler or Namath is incomplete.