The heydays of Marino, Montana, Elway, Young, Kelly, and Kosar had them going up against defenses that were allowed to do bump and runs and hitting receivers............and the rules were nowhere near as prevalent today when it came to protecting the quarterback. It gets even more lopsided the further back you go to the days of Staubach and Bradshaw.
However, in those days you had nowhere near the amount of parity seen today. In today's game, literally all teams have legit chances to get to a Super Bowl. In the 80s and 90s you had veritable all-star teams in the 49ers and the Cowboys, with teams like the Giants, Redskins, Bills, and Broncos trailing close behind.
Concerning Brady, if he isn't the best football player ever, then the guy who is barely eclipses him. No clearcut winner here.