Have you considered the InterContinental Tokyo Bay? It's nice, but not super luxurious. I stay there regularly and it has a lot going for it:

1. Spectacular views of Tokyo Bay, Odaiba, Rainbow Bridge
2. Large hotel rooms - similar to western hotels
3. Large bathrooms
4. Walking distance from the Hamamasutcho Station so you can hop on the monorail to/from HND

Usually a lot cheaper than IC Strings