I was looking for a way to delete a notebook from OneNote 2013 that is stored in OneDrive. Found some links, but nothing that was clear worked, and everything else was unclear. A few steps make it very easy:
1. Close the notebook in OneNote (right click > close notebook)
2. Navigate to your online OneDrive – onedrive.live.com
3. Navigate to your documents folder and find the name of the notebook you are trying to delete and check the box
4. Click on the Manage / drop down in the top row and click delete
