Best beach resort

I am going to Japan during late June/early July and was hoping to spend a few days by the beach as this will be only holiday of the summer.

Can anyone recommend a good beaches or places to stay? We will probably only have 3 days to relax by the sea!

Thanks.

Miyako is the best beach destination in Japan where I have been so far (I have only visited the main island, Miyako and the main islands of the Yaeyama Islands so far):
http://www.japan-guide.com/e/e7300.html

If you are staying in mainland Honshu, 2.5 hrs by train south of Osaka is the onsen resort town of Shirahama in the Kii Peninsula. It has some spectacular coastal scenic spots and a lovely beach.

http://www.nanki-shirahama.com/

I'd check out the Shakotan Peninsula area. It has a peaceful look to it, so I'd visit it if I was in the area.

http://www.biketoursjapan.com/cape_of_devine.html

As Uji says, unquestionably the best beaches are to be found on the Okinawan islands. However, with only 3 days, you probably won't have the time to get down there and enjoy them...

William5's suggestion of Shirahama is a possibility but like most beach resorts on the Pacific coast, the beaches can be overcrowded although at that time of year, probably not.

The Shatokan Peninsula suggested by Redds is certainly scenic, but you're unlikely to want to be sitting on the beach in Hokkaido as the temperatures will only be about 20 degrees...

You might consider the Japan Sea coast as the water is generally much clearer than the Pacific coastline. Somewhere like Suishohama in Fukui prefecture might fit the bill. http://www.kandou10.jp/en/spot/spot742_area03_7.html

However... the biggest likely obstacle to your plan is the fact that you want to be going to the beach slap bang in the middle of the rainy season... pretty much everywhere on the mainland during mid June to mid July is going to be getting a lot of rainfall; not really weather conducive to lounging around on the beach!

Anyway... hope you have a great trip!