But since I have to decide on a specific time of the year, I would say that the best time to visit Japan is during the cherry blossoms season. I am sure that it will be and experience you will never forget...
EXIF info:
Nikon D700
Lens: 24-70mm F/2.8G
Focal Length: 60mm
Aperture: F/20
Shutter Speed: 1/60s
ISO Sensitivity: ISO 320