I think my two favorites right now are Notability and Paper.
Paper isn't explicitly a note-taking app, but it's generic enough that I find it the best one I've come across for doing free-form diagramming, annotation and note taking. Organization is somewhat poor though. No sync (backup, but no sync, which is odd), and no search.
In practice, I tend to use Bear + Paper. Paper for collecting scraps, ideas, and allowing me to manipulate it like paper. I then migrate anything useful longer term out of Paper and into Bear. Bear does a better job being a bit of a scrapbook of things to refer back to, while Paper does a better job letting me manipulate things naturally.
I honestly haven't found an app that does it all by itself well. Maybe I won't.