If you see a hotel that has one price for rest and one price for stay, I STRONGLY recommend you don't stay there!
Unless you happen to LIKE mirrors above your bed . . .
Anyway, I second both the Toyoko Inn and Villa Fontaine recommendations. The only problem with most of the Villa Fontaine hotels is that they are not located close to the subway lines a tourist would use most often. It may require 2-3 transfers to get to where you want to go. There are some stations where you may need to walk a quarter mile or more between platforms.
There is another chain called Sunroute that sometimes falls under $100/night.
If you stay near a stop on the Yamanote line, you will almost always be able to access your destination with 0-1 transfers. The Yurakucho (pronounced Yoo-r/luck-cho) has a lot of good options for nighttime entertainment and is only one stop away (on Yamanote) from Tokyo station (where you transfer to Keio line that takes you to Maihama)
I would HIGHLY recommend using a bilingual
travel agent or asking a Japanese friend for help. There are hundreds of Tokyo hotels that won't pop up on the usual US sites like Kayak, Expedia, or even Google. Try searching for hotels on
http://www.google.co.jp/ and using a translation program. That's how you find the deals and cheap rooms in Tokyo (but not Disney owned hotels)
You will almost definitely need assistance with booking because these hotels don't have English websites and may be fussy with your credit card, though. I believe that JTB USA, JTB Hawaii, or H.I.S. might be able to help and I think it's free.