You should upload the notebook along with the sources of the actual article to the arXiv, of course.
The official (but rather hard to find) advice on this from the arXiv is to place your code in a directory called /aux/. (This is problematic for windows users.)
You can see an example of this in my recent paper on the extended Haagerup subfactor. A footnote in the text of the article explains that the code is available along with the source download. It would also be appropriate to use the comments field in an arxiv submission to explain that source code is available in the /aux/ directory.