I used to go to school on the US Naval base there so I know how you must feel. Currently, I live in Fuji, Shizuoka which is easily 3+ hours from where you are. I don't know anyone who speaks English and does magic in your area. However, I do know that there is a well established club in Kamakura. There might be some folks there who you could meet.
You might also ask at MagicLand in Kayabacho, Tokyo. firstname.lastname@example.org
Ton Onosaka, the owner, speaks fluent English. He is very busy so you might not hear back immediately.
Unfortunately, they don't have an English website (Japanese version is http://www.magicland.jp
Another place to ask is Magic House, run by Shigeo Futagawa. He also speaks fluent English. He might be able to point you in the right direction. Again, no English website but FWIW, http://www.magichouse.biz/
You can email him at: email@example.com
(also a busy person who may not be able to respond immediately.)
Hope this helps.
From the land of the rising sun. No strings or gimmicks. Performed every morning.