If you like pinball and live in the Bay Area, I highly recommend visiting Lucky Juju (aka the Pacific Pinball Museum) on Alameda. $15 admission for unlimited free play on dozens of pinball machines, including many vintage machines.
I saw One More Time [1] but that's about 4.5 hours out from Tokyo if my directions are correct.
Not pinball but there is this http://dgm.hmc6.net/
Dagashiya (local sweet shop) game museum
Satellite Lounge http://www.satellitelounge.net/
Reciprocal Skateboards - http://www.yelp.com/biz/reciprocal-nyc-new-york