When the sun starts shining and the sea warms up Odaiba Marine Park in Tokyo gets very popular. The park features the beach and a large boardwalk facing Tokyo Bay. Windsurfing lessons and equipment are available at the park. There is also a wakeboarding facility. It is located near Odaiba-Kaihinkoen Station, on the Yurikamome Line.
If you are very serious about windsurfing you can try a better location at Zushi. Located an hour by train from Shinjuku Station with the view of beautiful Sagami Bay Zushi beach has great waves and winds. Windsurfing equipment is available there for rent as well as surfboards and bodyboards.
Hachijojima, Niijima and Oshima islands that stretch from the tip of the Izu peninsula are popular destinations for intrepid surfers. But if you are willing to move further from Tokyo area the swell is better in Shonan. The coastal area in Kanagawa Prefecture is the epicentre of Japanese surf culture. However, if you're looking for truly serious waves move to the east coast of Chiba.
Surfing high season around Tokyo is the typhoon season between August and October.