I'm biased, but on an individual level I would put Peyton at #1. Super Bowl wins are a bogus way of rating QBs. One of Peyton's SB wins came during his worst year as a professional. He was honestly a bottom 5 QB in 2016, yet he won a SB. Peyton was consistently taking sub par teams to the playoffs, where they would often be bounced by better teams, with better coaches, and better defenses. Without Peyton, Indy would have been perennial top-10 drafters.
I wish that we had built teams the way Denver did for him. I would have much rather put an emphasis on defense with our first round picks, as we did this year and I hope to see Ballard continue to do. When you have a generational QB, he will make his receivers better. Peyton was regularly getting the same production out of Blair White, Austin Collie, and Pierre Garcon, as he did out of first rounders like Anthony Gonzalez and as unpopular as it may be to say it, Reggie Wayne. I do believe that Peyton had some say in how Polian drafted, and that's why we were consistently drafting offensive skill players in the first round. Believing that, I can't fault Polian entirely for the drafting, but I can't help but wonder what the team would have looked like if we'd drafted guys like Eric Weddle over Gonzo, or Demeco Ryans over Addai, or Nnamdi Asomugha over Clark.
Beyond the talent though, even the scheme we'd use on defense was infuriating. In Denver, they would press receivers and actually contest throws. The Colts defense would elect to give up 7 yard throws and then make the tackle. Why would a team with the best QB ever play such soft, bend don't break defense? Ron Meeks was the worst. It was the equivalent of having a relatively suspect offensive line, and forcing your QB to take 7-step drops 220 times, while taking 3-step drops a mere 90 times.
Anyway, bottom line is, Peyton is the GOAT. With a better coaching staff and smarter usage of draft picks, he would have retired earlier because he got bored with winning Super Bowls.