Kawagoe City
"Only 30 minutes from central Tokyo
A town of history retaining the culture and aroma of Edo, Koedo Kawagoe"
By their website (English)
http://www.koedo.or.jp/foreign/english/index.html

Ginzan Onsen, Yamagata
http://www.ginzanonsen.jp/index.htm
Small Onsen village. "Far, but it is worth a trip if you want to put yourself in real-old Japan life" ... by Kamei

Miyako-jima, Okinawa
Small Island in Okinawa. Not so famous yet for foreigner, so you can expact quiet and relax holiday.
You'll see the most beautiful sea in Japan.
Information (English)... http://www3.city.miyakojima.lg.jp/kankou-english/
Recommendable Villa ...
 Island Terrace Neela
   Built by sea. 20min by car from Miyako airport.
   They also have swimming pool, esthetic service.
   Quiet and comfortable villa.
    http://www.neela.jp/