I recommend Myoko Kogen in Niigata. It is not on a shinkansen (bullet train) line so it is a lot less busy to other more famous ski resorts on the shinkansen lines. You can read more about Myoko Kogen here (http://myokokogen.net/resorts/suginohara/)
If you prefer nice powder snow, I recommend Niseko in Hokkaido (http://www.skijapan.com/Home/Resorts/Niseko). It will be more crowded but the snow quality will be great!