Well, one thing I'd say is that even if the question was about each player being in his prime, it's still a very different question than who was the better player in an actual basketball game.
One on one, I might give the advantage to LeBron, who could certainly beat up Jordan quite a bit with his strength. And I'm not so sure that Jordan could actually out-quick James.
But considering who you'd actually want to have on your team in a seven game series, I think you take MJ every time (as well as a host of other players) over LeBron.
LeBron has had an impressive career, but he consistently came up short in Cleveland and it really took until he didn't have to "the man" on the team in Miami for him to win a title (not that Wade was better, but Wade still might end up taking the last shot in a big game).