If teammates affect a quarterback's stats so much, why does a stat comparison matter? Maybe the guy with lesser stats just had teammates who didn't catch the ball as well, which would affect most of the stats you listed, or defenses that gave up too many touchdowns, which would affect the win-loss stats. Or do the stats take into account how well the receivers catch the ball? Do they take into account how much pressure the quarterback was under when he made the throw (ie. how well the offensive line did)? I don't know football stats well enough to automatically say they don't, but I suspect they don't. And if they don't, how can you make an individual comparison based on stats that only partly depend on the individual?

Just to add, a hockey goaltender's stats do to some extent depend on the team as well, but not to the extent you listed for a quarterback. Sure, save percentage is a good indicator because it tells you what percentage of shots are stopped regardless of how many shots come at him, but a poor defense will allow more quality shots against. More odd-man rushes, more breakaways. An undisciplined team will take more penalties and allow more powerplay shots against their goaltender, which are harder to stop through screens. An inexperienced defense might cause more inadvertant tips, or might be less able to clear screening forwards out of the crease area, all of which make shots harder to stop. Better goaltenders tend to rise above the crop and compensate to some degree, but a goalie's win-loss record, his save percentage, and his goals-against-average aren't entirely based on his own performance. So if you want to debate, for example, Martin Brodeur versus Dominik Hasek, it's not as simple as comparing their stats.