Oh, this is my jam. Honestly, most of my finds come from diving headfirst into Archive of Our Own (AO3) and using the filters religiously. You've got to lock down the 'Alec Lightwood/Magnus Bane' relationship tag, sort by kudos or bookmarks, and then just start scrolling. The 'post-canon fix-it' and 'established relationship' tags are treasure troves. There's this one called 'A Consuming Fire' that absolutely ruined me—it deals with Magnus's father issues in a way the show only hinted at. A lot of the best writers have migrated there from FF.net, honestly.
I'd also recommend checking out Tumblr, weirdly enough. A lot of authors will link their masterlists, and you can find threads dedicated to recs. It's less organized, but sometimes you stumble on a WIP (work-in-progress) that's updated weekly and has a fantastic comment-section community. Just be prepared to lose a whole weekend.
Everyone talks about the fluffy domestic stuff, but I'm gonna go against the grain and say the best Magnus-centric fics explore his immortality as a form of trauma. Like, here's this guy who's watched everyone he's ever loved turn to dust, and then he meets Alec. Fics that don't just hand-wave that, but really dig into the fear—Magnus's terror of outliving Alec, Alec's quiet desperation to leave some kind of permanent mark on Magnus's endless existence—they hit different. They're less about grand demon battles and more about small moments: Alec learning a forgotten language Magnus used to speak, or Magnus finding Alec's old, mortal-age pension documents and just... staring at them. That weight gives the eventual fluff so much more meaning.
I also have a soft spot for the 'warlock Alec' trope, but only when it's done with consequence. Not the power-fantasy stuff, but stories where his magic is unstable or tied to his emotions, and Magnus has to guide him through a world that suddenly looks utterly different. It flips their dynamic in a fascinating way, making Alec the novice in Magnus's world for once.