The period you are going is good for Hokkaido due to both the autumn colors and harvest season. That being said, I doubt you are interested to take a plane or trains to get there.
This might be of assistance to you for activities:
http://www.japan-guide.com/event/Though, Tokyo being a metropolis has many events, art exhibitions, and things every other day. You can try Googling Tokyo Big sight, and other exhibition halls. Also check out Tokyo dome for activities.
There are a plenty of day trips from Tokyo.
I would recommend: Kamakura, Enoshima, Nikko, Nagano
You are looking for a place to stay overnight from Tokyo: Kusatsu, Ginzan, Karuizawa, Idaho
Lastly, I would recommend purchasing a 7 day JR Pass for the trip from Tokyo to Kyoto and back.
For your time in Kyoto, as it is pretty short, I would recommend spending the first day exploring Kinkakuji, Ryoanji, Ninnanji, and as much of Arashiyama as you can see.
The next day would be spent in central (imperial palace) and Eastern Kyoto (Kiyomizudera walk to Ginkakuji via Maruyama park and Philosopher's path)