Since nobody has mentioned this, it's worth pointing out that the PHT is on the western side of Shinjuku station, which is full of government and office skyscrapers and is almost eerily quiet at night.

The "crazy/busy" side of Shinjuku is the eastern side, particularly Kabukicho, which is packed full of drinking holes, nightclubs, massage parlours etc and is about as wild as Japan gets at night. (Which, at street level, is not particularly wild at all.)

All things considered, I'd go with the PHT. It's an awesome hotel, among the best in the world, and Shinjuku is just that much more convenient for getting out and exploring the rest of Tokyo. Airport access is good too, there's a direct limousine bus to the PHT's front door. Kid-friendly it may be, but I can't really recommend staying in Odaiba unless you've already been to Tokyo itself umpteen times and checked off the main sights.