Late September - early October ideas

Hi, I will be in Japan with my GF from 27 Sept - 8 October...mostly in Tokyo, with 2 nights in Kyoto.

Would love to hear about any special events/festivals happening in this time. Also, are there any day trips from Tokyo that we should take...ie leave early morning and return to Tokyo to stay at night. We are staying in Shibuya.

Also, if anyone can recommend any cool, small music/art venues in Tokyo where we could see some underground bands, that would be great!

Thanks for reading !!

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)

Specify the date here, please search.
http://www.gotokyo.org/search/en/event
Here also please refer to.
http://www.timeout.com/tokyo
http://www.japantimes.co.jp/events/
http://metropolisjapan.com/

"Idaho" ??

I think Josh maybe meant "Ikaho"?

Another suggestion for a day trip is to Mito, Ibaraki. The garden there is very beautiful, and nearby Hitachi Seaside Park has some great flowers if you like flowers or photography. At that time the Kokia may still be a bit green, but the cosmos should start looking nice!

For live music, here also please refer to.
http://www.tokyogigguide.com/en
Please look here for Art.
http://www.tokyoartbeat.com/index.en

In addition, see the HARVEST MOON event will be held from September 27 in the Sankei Garden of Yokohama until September 29.
http://www.yokohamajapan.com/upcoming-events/sankeien-garden-harvest-m...

Thanks a lot for the suggestions everyone, much appreciated!! :)

Thanks for the fill in Dragon. Would you happen to have been to Hitachi seaside park in different seasons and could provide me an opinion on each of them?