I have read a few S-Tier fantasy books but never came across an S-Tier science fiction book.

I start to believe there's no such thing as an S-Tier book in that genre.

Used to build @kiwi | https://macbudkowski.com/

"Tai Pan", "Noble House", "Shogun" saga
"First Law" saga (6 out of 9 books)
"Witcher" & "Narrenturm" series
"Name of the Wind" (very uneven but great overall)
"Catch-22"
"Shadows on the Hudson"
"I, Claudius"
"Hopscotch"
"Harry Potter" series (ofc targeted at young audience but still a work of art)
"Who is Michael Ovitz?"
"Masters of Doom"

+ some obvious classics like "Crime and Punishment" etc. and some Polish books that I don't even think have been ever translated to English

A simple model for an S-Tier book:

1) Great storytelling: right characters, tensions, action, plot twists, and so on.

2) Amazingly written: goes so smoothly that you feel almost a physical pleasure from reading.

3) Philosophical: makes you (re)consider some parts of your life or at least some critical viewpoints.