Last time I was there this seemed to become less true, most of the shops in the malls seemed to be taking VISA, and I saw quite a few promotional commercials about how visa was easier than cash, though this could be tokyo area only as I didnt get to go too far from my hotel in ikebukuro. That being said I would become uncomfortable with less than niman en in my pocket. And not every ATM will take a western bank card, but if you can find one that does, withdrawing yen directly will get you the best exchange rate.