Is there a way in the OneNote API (or Graph API) to interact with a OneNote document stored in a SharePoint document library somewhere?
Not the site notebook.
Thanks.
The OneNote API supports site-hosted notebooks. More details are in this blog post.
https://blogs.msdn.microsoft.com/onenotedev/2015/06/11/and-sharepoint-makes-three/
I'm not sure what you mean by SharePoint document library - isn't it the same as a SharePoint site?