Have not been but the video looks good for those who are looking for something modern and clean. Has a korean-style scrub down and hot stones bed as well.

Miyamaedaira Onsen
20 minutes from Shibuya
http://www.yukemurinosato.com/miyamaedaira.html
http://www.youtube.com/watch?v=ZMWmn2YwHhU

Price for adults is 1,200 yen weekdays, from 9:30 p.m. 950 yen, and 1470 yen weekends. 30 minute akasuri is 3,500
Hours
Weekdays 10 am - midnight
Sunday and Holidays 9 am - midnight.