Try IHG Strings Hotel in Shinagawa; careful with onsens
Love the Intercontinental Strings Hotel, on 24th-37th floors of a high rise next to Shinagawa rail and subway station. Typical small but super comfortable rooms. Great breakfast (especially when it is completely light outside at 4:30 am ... you'll be ready when buffet opens at 7...though the wait is hard)
Stayed there almost 20 times on business trips. Always dependable.
But visiting onsen resorts...I was not willing to scrub down standing up nude in front of hundreds of other guest just for the right to enter hot spring pool....