Hard to make firm recommendations as a number of factors come into play, including individual preferences, location, and price, to name a few. For myself, in general, I would rank them in the following order: The Strings, Tokyo (ANA), Tokyo Bay. But that's just me.

As for Narita, I usually stay at the HI Tobu Narita. It's just for one night (either coming or going), and this property has everything I need. But if prices were equal, or even a bit closer, I would stay at the CP Narita, which by the way has shuttles as well.