1) He is a different player than what MJ was. He is more Magic than MJ in his approach to the game
2) MJ had the best coach in modern basketball. Look what he did in LA. Clearly Jackson was aided by the talent he had the luxury of coaching, but 3 3-peats is unmatched in modern basketball.
3) MJ also had the luxury of having Pippen (and others), who is both one of the most underrrated players and greatest players of the last 30 years. What he did with the Bulls inbetween the three peats was incredible. When LBJ has been paired with someone in the same ballpark as, but clearly not as good as Pippen, he has won 3 titles in 5 years.
I am not a JBJ apologist, but I don't think the "dominance" you speak of, or lack there of, is as telling as what you portray it to be. In that comparison, circumstance and environment greatly benefits MJ.