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