Please, please DO NOT stay in Narita as a sightseeing base for Tokyo. Tokyo is full of wonderful things to see and you will be spending 4+ hours a day going back and forth on the train. Why go to Japan and then waste all that time not seeing things? It doesn't make sense.

Here's a specific Tokyo hotel recommendation:
The Comfort Hotel Higashi-Nihonbashi is directly on the Narita Airpot to Tokyo JR local train (not the express). You get off the train at the Bakuro-cho station (just a few minutes before Tokyo station), go through the exit gate from the train, go up exit #4 from the station to the street (all the exits are clearly numbered), look to your left, and there it is. It's even easier than getting to a hotel in Narita.

They have double-bed rooms for 10800 yen, two-bedded rooms for 13500 yen, cheaper if you have a discount like AAA to use. They have an excellent breakfast buffet that will cover part of your food costs. If you like walking, you can walk to quite a few places from there (Edo-Tokyo museum in about 15 minutes, Asakusa, Akihibara, and Tokyo Station (Imperial Palace) in about 45 minutes). These places are all also on cheap, direct subway or local JR train routes, so you would save considerable in transportation costs. Asakusa is really the only main sightseeing place that you can't reach by JR train from here if you are using a railpass.

It's very comfortable, quiet, and clean. They of course have private barthrooms. They have good coin laundry facilities. You can leave your luggage there before or after you check out. When you go onward on your journey, it's just a few minutes to Tokyo Station. (Which may, however, take some time to get from one track to another once you are in it--it's V-E-R-Y large.)

I think it's important to remember when you are travelling, that it's worth it to spend a small amount of money to gain a lot of time. Spending $20 more to have 4 more hours a day in Tokyo is a real bargain, IMO. Don't be itimidated by the logistics of getting places--you can figure it all out beforehand on the internet, there are Tourist info places in all the train stations, and people will help you on the street if you ask.

Having said all that, Narita is a wonderful little city, so if you have a few hours at the beginning or end of your trip, it's a fine place to spend half a day or so. It has really nice little shops and restaurants on a cute, winding main street, some very old house scattered among new but colorful houses, and a large temple complex that is well worth several hours of sightseeing. I guess there's also an open-air folk museum nearby, but I haven't been to it.