I'm a big Dormy Inn fan when I just need a clean room and I'm not looking for anything fancy. I especially like their Dormy Inn Premium and Onyado Nono brands (the latter having more traditional Japanese design elements while still retaining the value/convenience of a business hotel). Small rooms (<200sqft) but most/all properties have nice public bath/sauna facilities, free late night ramen and good breakfast buffets. I usually book via the hotels.com app when they're having a double stamp promotion (seems to happen about once per month) - typically about $60-80/night all-in with effectively every fifth night free if booking during the promo windows.
Here's are the Dormy Inn properties around Tokyo:
https://www.hotespa.net/dormyinn/eng...ist/tokyo.html
-FlyerBeek