One of the few hotels I know of in Tokyo with a 'rooftop' bath (apart from a true one at the Green Plaza in Shinjuku - although I suspect that the bath facilities for females at the Green Plaza aren't a patch on those for males) is at the Juyoh Hotel - a couple of stations from Ueno
http://www.juyoh.co.jp/

A mentioned regular comes here often. I imagine that bath time is switched between female and male guests but have never stayed here so cannot confirm.

I do hope you'll manage to make it to Mikoku Onsen in Ryogoku, yamakake. It may not have a rotenburo like Jakotsuyu does, but the atmosphere there was really special.