"Best" means so many things in science fiction - there are very few writers who can deliver both the science and the fiction convincingly.
With that in mind...
"Best" hard science fiction - Mission of Gravity (Hal Clement)
"Best" soapbox sci-fi - Starship Troopers (Heinlein)
"Best" future history - Foundation (Asimov)
"Best" sci-fi-yarn-you'd-tell-around-a-campfire - Santiago (Mike Resnick)
"Best" political science fiction - Dune (Herbert)
I don't think I could pick just one as the "Best science fiction novel".
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