Well, sure, Metropolis and Gotham are separate from NYC in-universe, but they're still based on NYC from a creative standpoint. There's that line someone said (maybe Denny O'Neil or Frank Miller) that Metropolis is the best parts of NYC in the daytime and Gotham is the worst parts of NYC at night. But what I'm saying is that I don't know if the comics' depiction of Metropolis was inspired by NYC prior to the Donner movie. Like how Smallville wasn't in Kansas until the Donner movie -- that very map reference you mention put it in eastern Pennsylvania or something, fairly close to Metropolis in Delaware.
Then again, I'm kind of talking myself out of my hypothesis right now, because it occurs to me that the very fact that that reference put Gotham in New Jersey and Metropolis in Delaware implies that they were meant to be similar to New York City. (Which is obvious in Gotham's case from its name; indeed, at least one early Batman story explicitly called the city New York.) I guess that stands to reason, since the comics' creators for most of its history were working out of NYC, and so had been the creators of the Superman radio series in the '40s. So it seems likely that the roots of treating Metropolis like NYC do go back that far after all.
In that sense, yes, I believe that Metropolis and Gotham had been inspired by New York in the comics for as long as I've been reading them. Huge, metropolitan cities, filled with blocks and blocks of skyscrapers are not really that common in the Western world. Most cities have urban centers that are only a few blocks with smaller buildings stretching out beyond that as opposed to New York which is many blocks are large buildings built close to each other. I wonder though, when Metropolis and Gotham were first depicted as being on an island near the coast, which is another defining trait of NYC.