I usually fly to Japan (Narita and Nagoya) at least twice a year for business and to visit family and friends. In fact, I'll be in Tokyo again at the end of this month for business. If you're looking for a nice, inexpensive place to stay which is in a good location, I would highly recommend the Asia Center of Japan (
http://www.asiacenter.or.jp/). It's within walking distance of Roppongi, a subway station, and a few convenience stores. You can request a room with or without a private bathroom. There are men's and women's bathrooms on each floor. There's the old annex and the new annex. Personally, I always request a room with a private bathroom in the new annex. The TVs require 100 Yen per two hours of viewing (this may have changed since I haven't stayed there in a while).
How will you get from Narita to downtown Tokyo? If you're using your JR Rail pass, do you know where to go to exchange your coupon for the actual rail pass? If not, I can help. I've done this before. If you need any advice on where to stay in other locations you'll be visiting, I can help there, too. I've travelled and lived in Japan for a total of almost six years. Ask away!
Have a great time in Japan!