Honestly? Top-rated is a bit of a moving target depending on what you're after. Sorting by kudos on AO3 is the standard go-to, but that can just mean the fics with the most mass appeal—often the popular tropes, AUs, or explicit content. There's this one with like 15k kudos that's a coffee shop AU, super sweet but maybe not the dark, complex dynamic you're craving.
I've had better luck filtering by bookmarks and then reading the comments. The real dedicated readers who leave thoughtful, paragraph-long comments tend to bookmark stuff with more layered character work. Also, don't sleep on Tumblr. A lot of writers will cross-post snippets or threads there, and the reblogs/comment chains can lead you to fics that maybe didn't rocket to the top of AO3 but have a fiercely loyal following. I found this incredible post-Shibuya fix-it fic that way; it's got maybe a third the kudos of the top fics, but the prose is stunning.
Sometimes the 'top' fics on FFN are older, from when the manga was in a different arc, so the characterization feels off now. The current hidden gems are often on AO3 with specific tags like 'canon divergence' or 'ambiguous relationships' filtered for completed works only. That's where the meaty stuff lives.