As for the defense, there is no denying how great the '86 Giants defense was. But in that Super Bowl it was Phil's performance that we all think about, not our defense. In Super Bowl's XLII & XLVI our defense surrendered less points than our XXI team did which was one of the keys to victory because our offense was incapable of scoring many points.
As for which one is best? They traveled different paths, played in different eras, and have different qualities. In the end Eli will have all the records to go with his Super Bowl MVP's, so barring injury, it's a pretty obvious conclusion.