Surf ski is growing little by little here, but compared to other countries, it's still pretty rare to find many other paddlers around the place. Having said that, if you're heading down Okinawa way and have flexible plans, one place that I do recommend is Amami Oshima. The local paddlers are mostly on SUP and surf ski and seem too get out most days. They'd be able to organize rentals I'm sure and, being such a small place, they'd look after you I think as well. They stock Think and Fenn skis and have some pretty good paddlers as well.
amami-occ.com
Around Tokyo, not really many places that will rent you a ski. There are a few other paddlers on this forum who live here too and might have other info, but as far as I know, most rental places are for sea kayaks. Having said that though, I'd definitely recommend the west coast of Izu for kayaking. Nishi Izu coastal kayaks do rentals and tours and the coastline around there is stunning! Caves and paddle throughs galore, with crystal clear water all the way around. Some really amazing coves around that way. Murata-san, the guys who runs NICKs is a bit of a legend too, almost a Japanese version of Paul Caffyn. He's very accommodating and will look after you well if you have the time to head out there.
www.nckkayak.com
Japan is a surprising good place to paddle so you'll have a blast. If you have any other questions, let me know.