As Japan has an absurdly small percentage of Christians, something that Americans in particular may not truly grasp, if you go, it is REALLY important for you to find a church to plug into... Being in Japan will very likely destroy you spiritually otherwise.
That being the case, I found this site (looking through it because I'm considering moving onto Japan after my contract expires here at GnB, though I may renew for one year before doing so)
http://www.jetchristianfellowship.com/
Granted, this is for Protestants only. I can't help Catholics, though my Catholic friend had no problem finding a church with a Latin mass when she was in Hyogo, just... nothing in English. This is a listing of English speaking churches in Japan, with listings for every region and possibly every prefecture (I didn't count them)
There are many denominations, so while you may not find your specific one, you should find something close to it, or at least one you are in agreement with enough to join if you're on the main Island, in any case. I think this resource is invaluable for any Christian who wants to start a life in Japan.