In Tokyo, most shops and restaurants accept credit card. In other cities (including Kyoto and Osaka), only about 30% of restaurants or smaller shops accept credit card. Chain store and department store usually accept credit cards, it's just the small mom and pop shop that are taking some time. The situation is improving fast though.
Online, I have a friend managing an ecommerce there with about 400 million dollar sales per year. Right now, 40% of the orders are cash on delivery. It was 60% of the orders three years ago.
Credit card is hard to get for foreigners (like usual) and for young people without stable jobs (banks tend to be rather risk averse).
I'm happy that Stripe is in Japan because the existing credit card providers are mostly incompetent and have really stupid apis.