Sabi, Japan has a very low (extremely low) crime rate. They have very high standards of public safety (the trains don't crash very often, the buildings are well-constructed, the cars have air bags), and there isn't the chaotic disorder of south east Asian nations. So generally I'd say Yokohama is one of the safer destinations of the world.
If you're refering to last year's qyake, tsunami and radiation exposure, see this other thread (but again I think a short trip poses an insignificant risk if any at all).
Phil at the safety hub over 6 years ago