I've got both. I'm sure that either cut is not exactly the same as the Singerverse. Singer did denounce elements of the first two as non-canonical. Personally, I'm leaning to: Superman: The Movie: The Richard Donner Cut
Superman II: The Richard Donner Cut
Obviously there is no Richard Donner Cut of the first superman, but he wanted the movie to end without the time travel. This works with Singers comment about the time travel scene from that movie not existing in his universe. He also said the magic kiss never happened, so again, leads to the donner cut of Superman II. Donner also said he liked the idea of people calling Superman Returns Superman III, if that even makes a difference.
See, I'm planning to watch the Singerverse before Crisis on Infinite Earths (and the other shows, Batman '66 and Black Lightning included). Currently I'm going with:
1948-197? ???? S Returns: Prequel: Book 1 of 4: Krypton to Earth
1997 ???? Superman: The Movie: Special Edition (alternate)
1999 ???? Superman II: The Richard Donner Cut
2006 ???? S Returns: Prequel: Book 3 of 4: Lex Luthor S Returns: Prequel: Book 4 of 4: Lois Lane
September S Returns: Prequel: Book 2 of 4: Ma Kent Superman Returns
The first movie happens slightly differently, like alternative dialogue shown in Krypton to Earth and no time travel. Other than that, it seems canon.
I could be completely wrong and the Lester cut is the right one though. For now this is what I'm going with.