What about the ANA and JAL hanger tours. They are a great 90 minutes each tour.
I did the JAL tour a few months ago, it was really neat to go to the actual hanger floor.
While I haven't been yet, there is also the Takubin tour. Japanese logistics company (like FedEx) - they have their factory tour at Haneda airport.
There is also a museum of flight on the airport grounds.
If you only have 4 hour layover, there are lots of neat ways to "hang" out.
They also have a great observation deck to watch landing and takeoffs.