You're touching on the fact that there are way too many variables that need to be factored into the equation. How good was their D? How good was their line and their receivers? How good was their team's running game? What was the quality of the defenses they faced, etc, etc, etc.
Obviously Brady and Peyton are two of the best of their era. I'm unwilling to talk about "best ever" because times change and even if you dominate your era, it doesn't follow that you would dominate every era - kinda hard to say how Unitas would fare nowadays.
I'm also gonna wimp out and say that if I had a must-win game, I'd be comfortable with either Peyton or Brady at the absolute top of their games. If that was a playoff game, yeah, edge goes to Tom Terrific.