much like aus most tracks I have been to in japan aren't easily accesible by PT.
The big problem isn't getting the train to near the track, it's getting from the station to the track. often we are talking 10 or 20kms. so by taxi you are looking at $60+ each way. and bus is not very easy to take if you cannot speak japanese.
having said all that. Mobara, Fuji, Tsukuba are all acessible from tokyo. and I'm sure there are more to add to that list that I haven't been to in the tokyo area. fuji speedway has access info on their website.