You can take a day trip to Nagano on the Shinkansen to enjoy the mountain scenery and walk down the interesting main street to Zengakuji. That was one of my favorite trips.
On my most recent trip, I had planned to go to Kawaguchi-ko (yes, it is possible by train), but I came down with a nasty virus on the first day in Tokyo and had no energy for more than one major activity per day. I had also planned to go to one of the Izu Islands, but I had to cancel, since most of the attractions there are on the outdoorsy side.
Have you been to Mito? Kairaku-en is considered one of the three greatest gardens in Japan.