I'm seeking a library that enables inline comments and annotations within a document. Can anyone recommend something?

That's highly dependent upon what kind of document structure you want to embed inline comments into.

What type of document do you need this for? E.g. Word, Excel, Markdown, plain text, etc?

HTML. Say, a blog post. Or a technical document. Instead of comment threads at the bottom, I imagine the comments inserted/attached inline in the text, perhaps only visible with mouse hover or appearing in a sidebar.