It depends where you want to go, and what you want to do. If you want to go skiing, for example, you want to go in the winter months to northern Japan where they have some great resorts. If you want to climb Mt. Fuji, you need to go sometime in the summer, usually around August, as it is only open for a short time.
There are also a number of beautiful tropical islands that are fantastic summer vacations.
I would not suggest early May, because that is around the time of Golden week and most Japanese are traveling home for this week long holiday. Perhaps the summer, or spring are good times. If you go early enough in the spring, you can catch the cherry blossom festivals which are a lot of fun as well.
There are things to do in Japan year round, so the time to go depends on what you want to do!
I would suggest to see the best of Japan go between May and August.
As internpete explained, it depends on what you want to do and see! Golden week is certainly much more expensive, and accommodation is tough to find.
If you want to ski or snowboard, then the winter months are certainly the best time to travel. The north eastern mountains on the Honshu island and the mountains in Hokkaido are covered in thick powder snow in winter.
For picturesque hiking and sightseeing - fall or spring is best for the majority of Japan. Seeing mountains covered in autumn colours, or sakura lined streets and parks is beautiful.
Hiking or tour-cycling around Hokkaido is best to do in late spring, summer, early fall - it's not as hot (usually) as in the more southern parts of Japan.
If you are travelling during the later summer months through Okinawa, Kyushu and Honshu, be prepared for *hot* weather, lots of rain and humidity - it's the wet season. The wet season makes the waterfalls spectacular.
For onsen hopping, I prefer the cooler - colder months. Cooking like a lobster in hot pools during hot, humid weather is not my idea of comfort!
There are many cultural festivals all over Japan - perhaps you can plan a trip around those that interest you, get a JR Pass and take the shinkansen between destinations.
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