Althought I love the first 3 Star Wars Films, I don't think I classify them as Sci-Fi. They actually more ressemble fantasy, I think, since the movies adhere to a pretty strict myth-hero archetype. If you discount Star Wars, the best Sci-Films are:
1) 2001
2) Blade Runner (Director's Cut)
3) Twelve Monkeys
Star Wars always struck me more as science fantasy, whereas 2001: a space odyssey is "hard" science fiction, very realistic. As such, I don't know if Star Wars and 2001 are fair comparisons: each have their own strengths.
But, strictly speaking, the best science fiction movie is 2001. Indeed, it is considered by critics to be one of the best movies--regardless of genre--ever made.