Funny- I watched this about a week ago. Not sure which version I have- the old one or newer one.
Does the movie have completely bizarre colors, including a purple tinge to flesh tones in many scenes?
[Screengrabs borrowed from DVDBeaver.]
If so, that's the first Blu-ray edition. If the colors look relatively sensible (aside from a teal push in some scenes), it's the "Filmmaker's Signature Series" remaster.
The first scene in NYC where Popeye and Cloudy are chasing the criminal- there was no attempt at beautifying the locations- trash everywhere. A documentary style film.
I remember NYC still being covered in trash well into the '90s.