PER is pace-adjusted and as I recall those leagues played at considerably higher pace. I find it pretty unlikely that Chamberlain could replicate his raw stats in the current NBA.
That said, his PER shows that a prime Chamberlain would be arguably the best player in the NBA in any year.
As for the original question, I think it's pretty clearly Jordan. Jordan is the only player I've seen who was able to go full-speed at both ends (by which I mean, carry an offense's primary scoring load while still being a high-level defensive presence) all game long. He wasn't doing that later in his career (he developed a regular season cruise control mode in the second three-peat) but prior to his first retirement, it was unreal how good he could be end to end.
The best two scorers directly after him, IMO, were Kobe Bryant and Tracy McGrady (before back injuries destroyed his effectiveness). Both were capable of spurts of defensive excellence, but neither could keep it up all game long, or even most of the game, while carrying a primary scoring load. McGrady did his best full-game defensive work as a Raptor when Vince Carter was the primary scorer and Bryant did his best full-game defensive work when Shaquille O'Neal was the primary scorer.
LeBron James is the closest thing yet that I've seen to Jordan in terms of being capable of doing that kind of work on the offensive and defensive end for the entire game. I think James is the guy who really compares to Jordan as a talent, not Bryant.
