Lindros played 10 seasons after already having his head turned to jello, and by that time it was an even lower scoring era than today. That considerably lowered his career PPG. He was at ~1.47e PPG after his first 297 games, which was the end of the '97 season. The '98-'04 seasons were all lower or roughly equivalent scoring seasons when compared to the years Malkin played. Malkin's career PPG is ~1.19, which Lindros had beaten if you take his career PPG through his time with the Rangers... it was ~1.21 for his career as of the end of '04. He played two more seasons, one with Toronto that brought it down to ~1.18, and the last with Dallas dropped it to ~1.14... so the career PPG argument is not really the best argument for Malkin, IMO.
Malkin would definitely not "blow him away" in points in the early 90s... it would be pretty close, with likely an edge (i.e. 10 points or so max) to Malkin, but they would be in the same tier offensively. While Malkin is not horrible defensively, he wasn't as good a two-way guy as Lindros, and he also doesn't come close to bringing the physical game Lindros had, which is something that really did matter back in the 90s. It is close, but clearly Lindros, for me. And yes, I am a Flyers fan... but Brind'amour was my favorite in those days, anyway.