First, a couple notes. As a rule, I favor peak over longevity when I make lists like this. Also, I'm not going to make any effort to separate the performance of QBs from their receivers unless noted otherwise. It may not be fair, but it's much easier.
First Tier
1. Roger Staubach
2. Steve Young
3. Peyton Manning
Of all the quarterbacks who started in the Super Bowl era, only three have been the league's top quarterback more than twice. All three rang that bell at least four times, and I consider them a pretty clear top 3. Manning is third because Staubach and Young add rushing value to their passing stats.
Staubach is ahead of Young because in my judgment Young played in an otherwise more talented offense, and more importantly because while neither won a starting job until about age 30, Staubach was held back by the Navy (saying nothing about his football ability) while Young was held back by losing the Tampa job to Vinny Testaverde (which is a knock against him). I guess you could throw the Heisman onto that pile as well.
I'm least confident in the placement of Manning, because he gets very efficient yardage; I've never seen anyone better at getting 7 yards on 3rd-and-6. Of course, what I've seen doesn't go back very far.
Second Tier
4. Johnny Unitas
5. Joe Montana
6. Dan Marino
7. Kurt Warner
8. Ken Anderson
These guys continue the list of dominant quarterbacks, with only a short drop off from the first tier. Unitas is closest to being on the first list, since I don't trust the numbers I have available from the early 60s as much as some of the more recent ones.
Montana's numbers are on par with the guys above him, but I rank him 5th because while he was usually A top quarterback he rarely THE top quarterback. Marino is a similar case, and gets relegated to 6th by Montana's superior postseason numbers.
Warner and Anderson get the last two spots because of their shorter careers (although I am impressed by Warner's ability to light up the world with two different teams. Anderson is the probably the guy I've ranked highest relative to the conventional wisdom of his era, based mostly on his statistics. Still, I'm concerned enough about that to drop him to the bottom of his tier.
Tier Three
9. John Elway
10. Fran Tarkenton
11. Brett Favre
12. Dan Fouts
These are guys who were the most valuable rather than the most dominant. However, inside the tier I'm ranking on my opinion of their peak. I was tempted to put Elway much higher, since I'm a big fan of his, but I'm trying to keep things unbiased.
The Rest
13. Len Dawson
Would be up with Anderson and Warner if I weren't concerned about the AFL talent level during his peak years.
14. Bart Starr
Threw so few passes that his sterling efficiency numbers are a bit inflated. Still a great quarterback.
15. Tom Brady
Would have ranked much lower before his magic 2007 season. As it is, his career looks like a hybrid of Troy Aikman & Bert Jones.
16. Troy Aikman
Was a peer of Marino, Elway, and Young from 1992-1995 but falls down here because of this much shorter peak.
17. Sonny Jurgensen
Old enough I don't know about him. Stuck him in about where his numbers warrant.
18. Jim Kelly
Just another quality quarterback. Longer peak than Bradshaw.
19. Terry Bradshaw
Number not amazing overall but had good peak years and a long career.
20. Bob Griese
I have the same concerns about Griese that I do about Starr.
21. Drew Brees
I don't like ranking players with most of their career still ahead of them. This is where I'd put him if he retired today.
22. Kenny Stabler
Just another good quarterback on a good team.
23. Warren Moon
One of history's great compilers. Threw a ton of passes but wasn't as effective with them as the guys ranked above him.
24. Boomer Esiason
Just another good quarterback.
25. Donovan McNabb
Just another good quarterback. Might be higher if he hadn't spent so much of his 2004-2006 peak injured.