Tokyo, Japan + Add a trip

I don't know about ryokans, but if you're looking for onsens, there are three exceptional ones. First there's the Jakotsu-yu onsen north of Kaminarimon alley in Asakusa/Ueno, which is open late and very local. There's another, larger and more spa-like Kannon Onsen near Senso-ji (in the park to it's left next to Sanja). If decadence is what you want, go for the 8-story Edo-themed monstrosity in Odaiba.

Tattoos are usually not a problem, unless you've got the full back tattoos distinctive to the yakuza.

I've been staying at Ryokan Katsutaro, in Ueno Park, and I can reccommend it. Ueno is beautiful and the Ryokan is a ten minutes walk from Ueno Station (you can take the Yamanote Line from there) and a two minutes walk from Nezu. It's very conveniently located, clean and it offers free internet access (wifi and lan). Part of the staff speak english, and everybody is very nice and helpful. They even took us to the subway station by car when we left, and helped us with the luggage and all. You can book via mail with no reservation fee.