Which months in Japan probability lowest of natural disaster?
There is no season for earthquakes or tsunamis. They can hit at any time of the year, and at any time of the day or night.

Typhoons happen in the warm season, but they will be forecast by the meteorological service, giving you time to move to a safe area.

If you want to go to Japan, just go. It is better to go in the season you want to go than to try and avoid earthquakes and typhoons, as they happen in random places out of anybody's control.