I've stayed at both the IC Tokyo Bay and Yokohama. Tokyo Bay is a really nice hotel and location, and I've found good rates there. It's convenient to Haneda and Tokyo Station, has a monorail stop outside or short walk to Hamamasutcho. Nice park and walking path outside, and the views from the Bay side rooms are really beautiful. There are a few restaurants nearby and of course it's near Tsukiji and Ginza and Tokyo Station. Nice if you want to be near the city but somewhere that's a little quiet.

IC Yokohama is not bad if you can get a good deal on points. Similar setup to Tokyo Bay in that it's on the ocean, nice walking paths and park nearby. It will be 45-60+ min into Tokyo by train so you need to factor in if that's worth it. If you plan any sightseeing in Yokohama or south of Tokyo then it's not as bad. There are plenty of places to eat around there so you can head back after a day of sightseeing and find enough there. Nearby is the Ramen museum, Cup Noodle museum, Yokohama Chinatown. Not as exciting as staying closer to Tokyo, and not as much going on late at night, but there's still plenty to do. It's reasonably convenient from Haneda, or a very long but single train ride on the Narita Express.