I think winning % for a QB is similar to arguing a pitcher shouldn't be a Cy Young winner with a losing record. I don't think you can necessarily say a QB is not effective if he's playing on bad teams. Eli's number that WILL hget him into the HOF:
All Time Passing Yards
1
Drew Brees
74,437
2001-2018
2TM
2
Peyton Manning
71,940
1998-2015
2TM
3
Brett Favre+
71,838
1991-2010
4TM
4
Tom Brady