Manning's problem was his team was not as good as the Patriots and Brady offset the advantage he gave the Colts compared to everyone else. If there is no Brady/Pats he wins 4 or 5 and he might be the hands down goat.
Same for Montana - no Simms and Giants and he wins 6 or 7 as he probably never is displaced by Young. Most people do not know Simms was 2-1 vs. Montana in playoffs. Those Giants teams were the best match for the 49er dynasty going 3-2 in playoffs between 81-90 against them.
Point is - ever great player/team has a rival that is a real test of what they are. For Manning and the Colts the Patriots were just better.