Any suggestion what to do in Tokyo for 3-4 days around September/October?

You could get to Kyoto, but that would make for a very busy 3/4 days. I would suggest staying in the Asakusa area because it's not so expensive, has lots of ryokan and of course then you can see Senso-ji temple. Of course you want to go to Shibuya and Harajuku, etc. A trip to Kamakura would be nice, especially as the weather is apt to be pleasant that time of year.