Some listed above I have never seen and I need to. With those gaps in my film watching noted, I am solid on my top 3 from those I have seen:
1. Blade Runner. I always wonder if the voice over cut helps a lot of people the first time, but after that I'd go for another cut. The visuals and world building are magnificent, and the pacing and plot fit it well. I love this movie.
2. Star Wars (A New Hope). I wish Rogue I had been made after Andor to more seamlessly fit with between the two. I like Empire more, but this one feels more important. If you stop with IV it also means you don't need to go on past V to VI in order to get an ending. Is it more of a western in space? Those were the defining toys of a generation, right?
3. Alien. Could probably be talked into Aliens. I need to rewatch them both and introduce my son to them. If non-goofy extraterrestrials are an important thing, then this has them.
And then it gets harder (to pick, not Sci-Fi-ness)
4. Fifth Element
and
5. Men in Black
Could go in either order or maybe one or both could probably be replaced by something else if you make me go rewatch a bunch of stuff. Both are ones I really enjoy actually watching. I think I judge sci-fi trying to take itself seriously a lot harder than I do the stuff trying to be fun when it comes to plot and faux-science.
Other possibilities...
Iron Man - ignoring the rest of the MCU, this is solidly sci-fi, right? I really like it. But if I get a super-hero list I will put it there and it saves me deciding if I want to make it 4 or 5 above and then deciding which of the current 4 or 5 to bump down.
Predator - I'm still disappointed our hero didn't blow up in the end. But, at first blush, it is the highest of the Schwarzenegger ones for me and if he had blown up too it might make my top 5.
And not...
2001 - Saw it recently for the first time (as noted in the Kubrick thread) and there is 45 minutes of a great sci-fi movie in there. Which is an hour and a half short of nailing it as the total package for being an all time great
Black Hole - Saw it when it came out as a pre-teen and apparently blotted out the end. Had fond memories of it and so saw it for the second time a couple years ago again. I now have memories of having fond memories of it.