Funny, I just came across a new crossover with 'Dungeon Meshi' the other day that really nails the tone. Honestly, finding the really popular stuff is all about following the trail of kudos and comments rather than sticking to one place. Archive of Our Own is obviously the main hub, and their tagging system is your lifeline—searching the 'Arknights' fandom tag plus 'Crossover' and then sorting by hits or kudos usually surfaces the big ones. But I often find that the actually popular stories in niche crossovers get discussed more on spaces like the Arknights Lore subreddit or specific Discord servers, where someone will post a link with a 'hey, this slaps' and it just spreads from there. Sometimes I'll just google 'Arknights x [fandom I'm into] fanfiction' and see what pops up from smaller sites or personal blogs; the webnovel scene in certain communities has some hidden, massively long-running crossovers that never hit the big archives.
An underrated tip is to check the bookmarks of authors you already like. If someone writes solid Arknights fic, their public bookmarks are often a curated list of other stories they enjoy, including crossovers. That's how I found a surprisingly heartfelt 'Arknights' & 'Fullmetal Alchemist' fusion that treats Oripathy like a form of philosophical alchemical backlash, which is a concept I'm still thinking about.