I've been to Japan several times and only stayed once in Shinagawa, which I would not recommend. The hotel was a ways from the subway station.

I think it has a lot to do with what you're used to but in recent years, I've been staying in the Minato part of town (Intercontinental, Conrad). Have also stayed in Shinjuku.

First and foremost, I'd recommend somewhere very close to a metro station, before anything else.

The next step is what part of Tokyo and what kind of environment. I like going to the busy areas (Shinjuku, Shibuya, etc) but I don't like staying there. It's frustrating to deal with that every time I walk outside of the hotel. But, it's different for everyone.