Maybe because I live in Australia, but Japanese beach season is very limited. First of all, you won't swim in north - too cold. In centre, most beaches are only open July - August. That gets better as you go down south. I think you can surf all year long in Okinawa and south of Kyushu & Shikoku, if you have an appropriate wet suits.
Besides, apart from Okinawa, Japanese beaches aren't that pretty for my taste. Especially on the main island, black pebble beaches are common. If you find a beach with white/yellow sands like that of Spain (which is still poor quality in my opinion), you should be very happy. And despite the poor quality of those beaches, they get packed during the season.
If you want a REAL beach experience in Japan, then fly down to Okinawa islands. You get a quality that could match SE Asian islands.