I second the suggestion of a mountain onsen instead. Get a good one for privacy, and if it's in the mountains you'll escape the heat a bit as well. Closest to Tokyo is the Hakone area but it will be filled with local tourists so secure a solid booking in advance.

I think this will be as restful as a beach stay would have been if there were restful beach stays on Honshu, plus you'll have an experience that really exists only in Japan.