We don't know.
The movie does not clarify whether Cliff killed his wife or not nor does the script provide any answers.
Tarantino himself will not provide an answer.
We don't see Cliff Booth kill his wife in Once Upon A Time In Hollywood, and nor do we see her death presented in any other form, which means that we're instead left to draw our own conclusions based upon what else we see and hear in the movie. And in that regard, Tarantino frames the key mentions of the death in a flashback, and the circumstances ostensibly just before it happens as a flashback-within-a-flashback. It's a hazy memory, which is our first indicator that things aren't quite as they seem.
So it's through Cliff's own flashback to those events we hear of it, and then within that he flashes back to the boat, where we see him arguing with his wife, Billie (Rebecca Gayheart), a harpoon gun sitting in his lap. There's no resolution to this moment: although things between the pair are clearly heated, and Billie is taunting him, Tarantino chooses to cut away before any violence (real or not) can take place.
The context of the memory, and the memory-in-a-memory, is important. This isn't a scene where a regretful Cliff is thinking about how he killed his wife, or at least it doesn't seem that way. It's instead him ruminating on how that ill-fated boating trip, where his wife did die in some way, has come to define his entire career, and that makes more sense if he didn't actually do it. We hear the waves at the end, which suggests this was an accident, albeit a suspicious one, and that makes the death of Billie a greater tragedy, but also makes Cliff's own story tragic as well.