For real, narrowing down the best Michael Afton and William Afton fics is tough because the dynamic shifts so much depending on the writer's take. The 'retrospective horror' ones where Michael is piecing together his father's crimes years later always get me. There's this one called 'Like Father, Like Son'—I think it's on AO3—that's a gut-wunch in the best way. It's less about jump-scares and more about the quiet dread of realizing your legacy is irrevocably tainted.
I'd also recommend looking for anything tagged 'Post-Sister Location' with a heavy focus on Michael's physical and mental decay. Those stories often have William as a lingering presence, either as a ghost, a memory, or something worse whispering in the remnant. The body horror mixed with psychological torment is peak FNaF fanfiction for this pairing, honestly. It's a niche, but when it's done right, nothing else hits the same notes of grotesque family tragedy.