It's hard to find good Wi-Fi access in Japan. Why? Please read this.
Japan Times
Simple answer is we don't need it and we think we should pay for that. If you pay, you can find Wi-Fi everywhere.
However, there are some companies providing free Wi-Fi these days. The list has only major ones.
Seven Eleven shops
Need registration. It seems much easier to resister it at the shops. Just connect their Wi-Fi network in a shop and follow instruction.
JR EAST
This one has good English instruction.
Wired Cafe
Ok, they don't have English website. Don't need registration for this one.
I will add links when I find good ones.
