Best score in the Star Trek franchise
I will start with a significant caveat: I don't really know music from the last, say, 5-6 years of the franchise (after Beyond I haven't watched much). If somebody wants to advocate for some of the recent stuff, be my guest, I will give it a try.
Personally I think there are four candidates:
TOS: "Amok Time" - I think Gerald Fried's score for the premiere episode of S2 is amazing. It's exotic, exciting, unique, and has had a stunningly long life in our culture. It is small in scale compared to the other candidates but eminently effective nonetheless.
TMP: The shadow cast by Jerry Goldsmith's effort in the first movie covered the franchise for the succeeding 25 years and still resonates today. The main theme obviously carried over not just to several movies but a whole other TV series. It was never played with more verve and panache than in those first recordings, though. Beyond the iconic main theme, you have the Klingon music that was also used in future movies and TV episodes, the haunting Ilia theme, the blaster beam, etc.
TWOK: James Horner's freshman effort for a major studio film is arguably also his best. If nothing else, it establishes some of the iconic phrases and textures that he famously borrowed in future works. If it also borrows from work by other composers (especially Prokofiev) it doesn't rise to a level I would call plagiarism. What he does is perfectly accentuate the dramatic tension of the most heart-pounding (and eventually heart-breaking) moments in franchise history.
TUC: Maybe a bit of a dark horse (and not my personal pick, just one perhaps deserving of a spot on the podium). Director Nick Meyer (as he did on TWOK) once again pulled an unknown composer out of obscurity, explained the sound he wanted to hear (inspired by Holst's The Planets), and let Cliff Eidelman create a dark, brooding, totally unique score in the Star Trek pantheon. That Eidelman (unlike Horner) was unable to build a lasting, important career from this terrific beginning is a shame.