ST: WoK is a very good movie, and -- for soft science fiction -- the Star Trek universe actually does a pretty good job portraying science. At least, when the writers are having a good day, they bother to paste over the magic with sciencey words; for instance, inertial dampeners and Heisenberg compensators. That said, Wrath of Khan doesn't even make my top 10 science fiction films. It might not even crack the top 25.
Possibly because I saw the original broadcast on PBS, the 1980 made-for-TV version of Lathe of Heaven is near the top of my list. It was unavailable for a very long time, and was kind of legendary among Ursula LeGuin fans. After decades of being asked for a rebroadcast, the folks at PBS finally got the rights back, located a pretty good print, and offered it (on VHS) as a pledge premium. Watching it again for the first time in 20 years, it held up surprisingly well. It involves ideas that are explored (in very different ways) in movies like Tron, The Matrix, Paprika, and (the execrable) Inception. It works very well as science fiction, the central idea is well presented and there are no holes too large to bridge with a willing suspension of disbelief. The hero is sympathetic and solidly heroic. The villain is terrifyingly believable.
(Paprika is also a very good movie that is better science fiction than Wrath of Khan)
Gojira, the original version of Godzilla w/o the inserted scenes with Raymond Burr, is also way up in the rankings. Its good-enough science fiction and Serizawa Daisuke is an amazing character. I can't think of any portrayal of a scientist with a doomsday device that is as sympathetic and moving. In fact, all of the principal characters are well written and well acted.
Them is the best magnified animal menace movie ever made. The science content is pretty slight, but the story is so good and the performances so much fun, that it is impossible to care.
The Martian is a very good piece of hard science fiction, and very satisfying drama.
Also ahead of Wrath of Khan on my list (off the top of my head, and in no particular order):
Some cut of Blade Runner (I like the ones with the voice-over narration), Village of the Damned, Quatermass and the Pit (5 Million Years to Earth), Day of the Triffids, Invasion of the Body Snatchers (1956 and 1978), When Worlds Collide, Rollerball (1975), Arrival, Andromeda Stain (1971), Ghost in the Shell (1995 anime), The Thing (1984), Logan's Run, The Fly (1958 and 1986), Scanners, The Omega Man, The Incredible Shrinking Man , Deep Impact, Marooned, ... okay, I am a huge nerd.