I just got back from the Kansai area, a night bus ranges from 4000 – 8000 yen one way but be prepared for a long journey back to Tokyo. It was a fun experience though and I didn’t have too much trouble sleeping and there were plenty of regular pitstops for food etc. along the way.
A shinkansen on the other hand is upwards from 12000 yen one way but is obviously much much quicker – it cuts down your travel time by more than half.
So it really depends how quickly you want to get to your destination and what your budget looks like. Hope that helps!