The most recent issue of J-Life
had a list of schools it recommended. I couldn't vouch for any of them, but in addition to the likes of Tokyo, they list places in Fukuoka (City), Nagano, Gifu, Osaka, Okayama, Kobe, etc. etc.
The list starts at pg. 12 (pg. 14 going by PDF count). It's a large file so it takes a while to show up, or at least, it does on my work computer.