I agree that 4/6 is more impressive than 4/4. At first, it seems like 4/4 is better because you never failed on the biggest stage. However, 4/4 vs 4/6 really means the 4/4 guy failed even earlier, in a less impressive game! In other words, they failed to come up in the clutch when it should have been easier to do so. To get to 6 superbowls means you had to come in clutch in 6 conference championship games, not just 4.
Now quick aside - in reality, especially in football, we probably ascribe too much importance to winning superbowls, since its a team sport with huge rosters, no 2 way players (so offense is only half and defense is only half, both divided by about 14 rotation players), and the playoffs are single elimination, so luck plays a bigger role. So it's hard to really evaluate and separate a QB from the team's performance and luck. But, for the sake of this, let's equate QB "Greatness" with winning. Additionally, the more important the game, the more "greatness" points you accrue.
So back to QB greatness, accepting the premise that team wins in the post season really directly demonstrate QB greatness. Let's say making the playoffs is worth 1 point. Then winning the wild card game should be 2 points. Well there's our first problem; by being WORSE in the regular season, you could actually get an extra game and an extra "Greatness point." But it's clearly better to get a 1st round bye. So a first round bye has to be worth at least the same as a wild card win, because a bye and a WC win both get you to the Division Round. But it's worth a little more too because you got your team some rest. So 3 points for a first round bye. Then 5 points for a division round win. This means you make it to the conference round with either 9 points (for a bye and a Divisional Round Win and making the playoffs) or 8 points (making the playoffs, WC win, Divisional win). Then say 8 points for a conference championship win and getting to the super bowl. 12 points for a superbowl win. Therefore, a superbowl winner from the wild card slot gets 12+8+5+2+1 or 28 points. A superbowl winner from the 1st round bye gets 12+8+5+3+1 or 29 points. Superbowl loser gets 16-17 points. Let's look at some famous and not-so -famous QBs:

It's actually not a bad ranking, considering I made up the scoring BEFORE I saw how the ranking would come out. There's other things you could do, like add more QBs, add points for MVPs, Superbowl MVPs, etc, but that would add more time. I'll try to later. Maybe you could add a modifier for QBR or something to account for yards, TDs, completion percentage, etc. But the rank order is not that bad for "QB Greatness."
Brady comes out awesome. Bradshaw and Montana are studs. Peyton gets pretty docked, and it's clear to see why compared to Brady: lots of playoff appearances, but Brady's won 9 (Nine!) Divisional games, 6 Conference games, and 4 Superbowls to Manning's only 4 division wins (so thats 45 points for brady and 20 for manning), 3 conference games (48 to 24) and 1 superbowl (48 to 12).
This system HATES Marino, but I was actually surprised not that he hadn't won a superbowl (obviously I knew that), but how little playoff success he really had. Not like he was going deep every year like Barkley or Malone; he was just not doing much in the playoffs for how good he was.