My wife & I generally go to Japan every year to visit family. The food is awesome, the trains make it easy to get around Honshu the main island, renting a car & driving around Shikoku is best imo.
East of Tokyo, the Chiba prefecture has waves all along it. Above there does too, but its close to the Tokushima nuclear disaster & best avoided. Above there has some of the best waves in Japan, but the infrastructure has been destroyed by the tsunami. Below Chiba prefecture is the bit pointing out. The Izu peninsular has great waves South of the end, round from Shimoda. Lots of little sandy bays & a number of outer islands you can reach by Ferry that have good waves. Then there is a big gap in waves along the coast & you wouldn't want to surf there anyway. Coz the Nagoya prefecture is the most heavily polluted area of Japan. This is where the big manufacturing places began & still remain. There are waves on the South end of Honshu, the Wakayama prefecture, but its just as easy to head to the best area, Shikoku.
For a first trip to Japan Kamakura, just below Tokyo keeps things pretty simple & allows you to check out all the other cool stuff Japan has to offer. The owner of a surf shop posts video's of the surf there on his youtube channel fairly regularly.
/videos
The Shimoda area is also very easy to get to along a scenic coastal trainline running as far as Shimoda with a short taxi ride to hotels round by the surf which is busy on weekends.
The beer however, although it goes down great & tastes good. They have some of the worst beer for hangovers imo.