Yes, the goalies and players were worse back then, but it's not like anyone thinks Gretzky would score 92 goals and 215 points in today's NHL. Everyone unanimously agrees his stats are "inflated" due to the era he played in.
That said, he's still the best. He would absolutely lead the league in points in today's NHL, and by a decent margin. Eras overlap, and that overlapping is the proof needed to back up this claim.
97-98 was the 4th lowest scoring season in the modern era. Top goalies were guys like Hasek, Brodeur, Roy, etc... Top Dmen were Blake, Lidstrom, Pronger, Neidermayer, etc... Top forwards were Jagr, Selanne, Bure, Forsberg, a 36yr old Gretzky who finished 3rd in league scoring, etc... These are guys who were all-stars for years after Gretzky retired, and he was right up there with them. At age 36, Gretzky was well past his prime (like all players), so it's easy to make the connection that he would score more and dominate more had he been in his prime at that time (97-98). And since some of those guys also went on and competed alongside the top guys of today, you can conclude Gretzky would have also dominated now - even if it wouldn't be by stupid margins like before.
TL;DR - Gretzky is #1