OneNote Notebook migration is not possible at this time.
When you attempt to migrate OneNote notebooks with SharePoint they are converted to folders, and the sections and pages in the notebook are migrated as a .one package. This means that the information is still accessible, but it will not be in a usable form.
There is no solution or workaround to this issue.
The content type associated to a OneNote notebook is Folder in SharePoint (visible through All Properties in Copy Content). Due to this behavior, it will be handled as a folder by Sharegate during the migration process.