Good luck on your trip. I loved it in Tokyo. TFP members were really helpful with their advice on my trip. It was so much fun!
Craven did a great job, but I will add a couple more.
I stayed at
Grand Takanawa Prince . It's a 5 minute walk to the subway/ shinkansen. Also, there is a great Indian restaurant (Devi) near the base of the hill where I ate my first night in Toyoko. My roommate was Indian and said that it was just like being home. The hotel has a good reputation on the Flyertalk forums. The gardens in the hotel are serene.
Toyko Imperial Gardens : Seeing seas of people in white manicuring the landscape by hand was cool.
I never made it to the
Yasukuni Shrine, but wish I had especially since I've spent so much time in China. It houses the souls of Japanese solderers including war criminals and features some
revisionist history. Visits by Japanese politicians always piss off Asian nations.
Many restaurants will have pictures or models of what there is to eat. Also, check out the basement of the department stores to load up on Japanese food at a fair price. There will be delis/ bakeries and such.