I think Marlon Brando was the first, actually, to negotiate a payday that was earthshaking in the industry. In early 1975 Brando signed on to Superman: The Movie with a salary of $3.7 million and 11.75% of the box office gross profits, totaling $19 million. That was for five minutes of screen time. Those numbers may not seem huge but in the mid '70s, on an inflation-adjusted basis as compared to even 1989, they were massive. America was just about to come off the gold standard (May of that year), so the dollar had not yet begun to depreciate. While Nicholson's numbers for Batman were impressive the dollar by 1989 was already worth nowhere near as much as it was in the mid '70s.

Anyway, whether Brando or Nicholson made "more" is beside the point. Brando blew the doors off when it came to actor compensation. I don't recall another actor getting that kind of back-end deal until Nicholson for Batman, actually.