Thanks for the replies so far.

We've put our heads together a bit and decided that instead we'll head further out of Tokyo (Hiroshima, Miyajima or Beppu?) for two nights and then head back up to a ryokan/hotel near Narita so we're not stressed for our morning flight.

So Hiroshima, Beppu, Miyajima and/or Narita ryokan recommendations are welcome!