I almost hate to recommend this place because I don't want it to get crowded, but I really like 森林風呂 in Jiaoxi, Yilan. It's just as you describe. It's segregated by sex, as one would expect with a naked hot spring. It has pools with a variety of temperatures and a sauna. Bring your own towel, or you can rent one. They have lockers inside for your personal belongings.