I also recommend a day trip to Nikko. I believe that it was about 50 minutes or so from Tokyo Station via the shinkansen to the connecting station for the local train to Nikko. The local train takes about 40-45 minutes or so from there to Nikko. A very nice day trip.

Even better though might be a day trip to/through the Hakkone Region. You begin in Odawara. The Shinkansen from Tokyo to Odawara is about 35 minutes. At Odawara station you can buy a Hakone pass (a two day pass a few weeks ago cost us 3400 yen pp and was a fabulous deal). The pass allows you to travel through the region on just about all of the various types of transportation. From Odawara, you connect to the Hakone train. That's a short ride to the connecting station where you hop aboard a tram. That's an interesting ride that snakes through the mountains. Then from there you change to a funicular which takes you further up into the mountains. Then from there you hop aboard the ropeway (think ski-lift gondola/tram) that literally takes you from mountain peak to mountain peak, along the way providing magnificent views of Mt. Fuji and the surrounding area. Along the journey, you can get off and on at whatever stops you like, to check out the sights. I recall that one stop in the mountain-tops had thermal sulfur springs (sort of like at Yellowstone Park in Wyoming). The ropeway ends down near a big lake. From there you take a replica of a galleon ship (looks like a pirate ship and is a bit cheesy looking, but it is nevertheless fun) across the lake. When you get off the ship there are buses there that will take you back to Odawara station. The whole circuit is set up quite nicely so that it is designed to be simple. All of the connections might sound a bit intimidating, but trust me, it is very simple. You can do the circuit as quickly or as slowly as you like. The entire circuit took us about 4.5 hours from Odawara, but we were on a very leisurely pace and stopped at a few points for snacks, shopping, and just soaking up the sights. That day trip is one of my fondest memories of Japan.