Actually, the Phoenix books were towards the end of the Bantam run...
Not really. If we discount 1970's Spock Must Die! as an outlier, Bantam's line of original Trek fiction began in 1976, and The Price of the Phoenix was the third book they published in that period, after The New Voyages and Spock: Messiah! So that one was very early in the run. The Fate of the Phoenix was two years later, in '79, and was the fifth-to-last book they did.
No, I'm specifically thinking of articles where someone would say something like, "The best of the novels are The Wounded Sky, The Final Reflection, the Piper books, and the Phoenix novels." It wasn't just a "Best of Bantam" sort of thing--these people were writing in the Eighties, with the Pocket line already going strong.
Considering how much praise the Piper duology got as well, it occurs to me that this particular audience, (probably) made up mostly of fans with a Seventies mindset, might've gravitated more to those novels with a heavy fanfic sensibility to them--the K/S undertones in Phoenix and the Mary Sue approach in the Piper novels.
I agree that they were drawn to books that felt like fanfic, but dwelling on K/S and Mary Sue is oversimplifying what that means. A large part of it was the difference between the authors who were Trek fans doing it out of love and striving to reflect something of the spirit and emotional impact of the show and characters (however awkwardly) and the ones who were professional SF authors for whom it was a paying gig and who maybe didn't capture those more visceral and intangible aspects. (Of course, these days, mostly you have professionals who are also lifelong fans doing the books, so that distinction no longer applies.)