As you can see on Wikipedia, temperature in Tokyo is mild in October and getting chilly in November. I think it will be the most comfortable season with a proper outfit there. Kyoto is bit cooler but I don't think it's an issue.

October is bit cloudy in Honshu region because of an autumn rain front, however, not a rainy at all, no issue in my opinion.

If you prefer sight seeing in Kyoto with beautiful autumn leaves, the beginning of November will be a good timing. However, I have to warn your that Kyoto will be fill of tourists both from inside and outside of Japan. I would suggest booking transportations and a accommodations earlier.

Hope it helps!