I think Tokyo still has too many cars (and plenty of two or three lane roads) and Japan as a whole isn't really bicycle friendly. The city is very dense however and the cost of parking spaces makes cars only accessible to upper class families.
Have done this in Tokyo, Osaka and Nagoya and they have been fantastic cities to bike commute in.
Cycling in Tokyo is a bit of a mixed bag in my experience, some streets have bike lanes, some have a bicycle strip on the main road (though this is often shared with temporarily parked cars), sometimes bicycles need to share space with pedestrians. Signage is often unclear.
I guess calling it bicycle unfriendly is a bit harsh, but at the same time it often feels that bicyclists rank third behind cars and pedestrians.