Pro-Football-Reference has data from before 1970 and 2006/2007 so they are taking another shot at ranking them in both top single seasons and career performances.
A whole post is dedicated to the methodology used so read it if you want to criticize the way the list turned out. Basically it's yards per attempt adjusted for sacks, TDs and INTs, minus the league average, times attempts with rushing thrown in if the QB was a solid contributor on the ground (over 4 YPC).
Peyton Manning recorded the 2nd, 11th, 29th, 31st and 42nd best QB seasons in NFL history. Other active (or recently retired) QB seasons in the top 50:
Tom Brady 2007-3rd
Kurt Warner 1999-8th
Daunte Culpepper 2004-12th
Jeff Garcia 2000-14th
Drew Brees 2006-28th
Kurt Warner 2001-32nd
Donovan McNabb 2004-40th
Daunte Culpepper 2000-41st
Steve McNair 2003-49th
Manning ranked as the top QB in the league for 4 consecutive years from 2003 to 2006 one of only 3 QBs to top the league more than twice.
The top QB in each of the last 15 season
Quarterback Year Team ANY/A Rating
Tom Brady 2007 NWE 8.04 1817
Peyton Manning 2006 IND 7.38 1396
Peyton Manning 2005 IND 7.44 1189
Peyton Manning 2004 IND 8.82 1885
Peyton Manning 2003 IND 6.85 1220
Rich Gannon 2002 OAK 6.55 1072
Kurt Warner 2001 STL 6.79 1189
Jeff Garcia 2000 SFO 6.81 1354
Kurt Warner 1999 STL 7.53 1490
Randall Cunningham 1998 MIN 7.78 1324
Steve Young 1997 SFO 6.98 904
Brett Favre 1996 GNB 5.94 707
Brett Favre 1995 GNB 6.62 1040
Steve Young 1994 SFO 7.53 1407
Steve Young 1993 SFO 6.96 1262
And finally the top 20 career values (this is career to date for active players. They can rise or fall in the coming years.)
rank QB att rate
1 Dan Marino 8358 8593
2 Peyton Manning 5405 7946
3 Steve Young 4149 7739
4 Fran Tarkenton 6467 7140
5 Joe Montana 5391 7006
6 Dan Fouts 5604 6672
7 Johnny Unitas 5186 6211
8 Ken Anderson 4475 5974
9 Roger Staubach 2958 5680
10 Len Dawson 3741 5604
11 Brett Favre 8758 5107
12 Norm Van Brocklin 2895 4688
13 Sonny Jurgensen 4262 4525
14 Otto Graham 1565 4250
15 John Elway 7250 4123
16 Bart Starr 3149 4101
17 Boomer Esiason 5205 4013
18 Kurt Warner 2959 4004
19 Tom Brady 3642 3845
20 Roman Gabriel 4498 3844
The active or recently retired players that appear between 21st and 75th:
22. Trent Green
28. Steve McNair
29. Jeff Garcia
33. Daunte Culpepper
38. Donovan McNabb
42. Mark Brunell
51. Drew Brees
52. Vinny Testaverde
59. Brad Johnson
65. Carson Palmer
74. Marc Bulger
75. Doug Flutie
So in only 10 seasons Peyton Manning has thrown for the 2nd most value in NFL history, had 5 of the 50 best seasons for a QB ever and been the best QB in the league in four straight seasons. Peyton is likely only one more Peyton-level season from passing Marino for the title of best QB in NFL history.
They also did a worst QBs post, but we wouldn't know much about that here.