Tenjin Reader is a heavyweight website loaded with options to help you understand and study from Japanese reading material. You can copy/paste text into its reader, which then adds furigana and changes its formatting. Clicking on words within its database will pull up a dictionary definition as well as a few choices:
Add to SRS will put that word's information into a WaniKani style review queue.
This allows you full customization of each item's information and a section for adding your own notes.
Other tabs have similar features for sentences, kanji, and the ability to import your WaniKani vocabulary, so you can make your own lists to study from outside the app.
Tenjin Reader is slow and chugs to get through data you feed it. The supplied content also seems to contain lots of bugs that haven't yet been worked out. But the site shows promise.