The FBO in Narita is pretty much the only one in the entire country as far as I know, and they charge about $3,000 to use it each time in addition to all the other fees that you'll incur there.
As far as an FBO at Nagoya, there isn't one at Centrair (RJGG) but there may be one at the old downtown airport that I'm unaware of.
I can remember using a facility at Kobe that resembled an FBO, but not sure if that was available for use by the public.
There are plenty of handlers available at every airport in Japan and they all give good service. My personal favorite is JAS.
Hangars for business jets are also extremely difficult to come by in Japan. You can get one for Maintenance, but getting one just to use for overnight storage is almost impossible. Sometimes your handler might be able to get one to use for "Maintenance purposes", but if you do this repeatedly the authorities eventually figure it out and will put a stop to it.
If you are looking for a Hangar for long term use it is highly unlikely you will be able to find one in the Tokyo area.