June is probably one of the worst months to be in Japan for landscape shooting since it is the month of the Japanese Monsoon...
- the chance of heavy rains is highest
- the air is humid and lacks transparency
- it is pretty hot and can become very uncomfortable at times if you are not used to such weather
- some higher mountains can still be snow covered and require crampon/ice axe knowledge for safe travel
Amidst that, Hokkaido is indeed the area least affected by the adverse weather conditions. Hokkaido doesn't have really spectacular mountain scenery in itself, but areas like Shiretoko or Daisetsuzan are interesting.
Beware of the bears though, a trekkers got killed 2 weeks ago again.
Overall though, I would personnally focus more on man made structures if June is a given.
Cheers,
Bernard