We stayed in Ikebukuro which is a bit of business district however we got a great deal with the hotel when booking through Expedia and got our room upgraded when we arrived too. As Tony mentioned, it's well worth getting the bullet train and if you fancy stopping off at a couple places then the Japan Rail Pass is well worth it, even if it is a bit of a faff booking all of your train journeys when very few people speak much English.
In Tokyo then I recommend going out to Harajuku and Shibuya on Sundays, it's an interesting experience to say the least. If you do venture out of Tokyo then I strongly recommend Takayama which is up in the Japanese Alps, the train journey there is amazing. We also went to Kyoto, which I was slightly underwhelmed with, Osaka which was a bit more laid back than Tokyo and Hiroshima which, as you can imagine, had a very sombre atmosphere, but strangely was probably the nicest looking city we visited while we were there.