If you're looking to explore Tokyo, I'd suggest Shinjuku. For Odaiba, you just have to take the monorail in/out almost every time. It's a hassle and it's expensive.

If you're looking for an easy time with kids, Odaiba is good as the malls are interesting and there are a couple of "kid friendly" places on the free shuttle service that circles around Odaiba. You could spend a day or 2 doing that, and then another day going into Tokyo.