I’m not sure of a definitive SF mystery/whodunit, but here are two that were nominated for Hugos recently:
Six Wakes: A starship’s crew has been murdered. Their clones wake from hibernation and desperately try to figure out whose original was the murderer, and if their clone is also murderous. Great premise for a thoroughly standard-structure whodunit.
Too Like the Lightning: This is some weird shit, focusing like 70% on a bizarre future world, 20% on the nonlinear structure of the novel, and 10% on a series of mysterious hovercar deaths which may or may not be purely accidental (spoiler alert: c’mon, you can guess). The narrator is the worst mass-murderer in human history in several decades, but you don’t find out what exactly his crimes were, or why he committed them, until much later. The whodunit is central to the book’s plot, but the book’s plot isn’t really central to the book, if that makes sense.