You may find the free Wi-Fi Hotspots in Tokyo. Before booking the hotel in Tokyo, I recommend you check if the free Wi-Fi can connect at the room.
In addition, you can use the Wi-Fi at the following places. However, it may be difficult to connect to the free Wi-Fi hotspots stably, depending on the environment of Wi-Fi Spots. If you make a business trip to Japan, I do not recommend the use of the free Wi-Fi Hotspots due to the security reason.
JR Train Stations
*The user registration will be needed before connecting to the Wi-Fi.
JR EAST
http://www.jreast.co.jp/e/index.html
https://www.jreast.co.jp/e/pdf/free_wifi_02_e.pdf#search=’wifi+JR’
JR Central
http://english.jr-central.co.jp/info/wireless/index.html
Starbucks : http://starbucks.wi2.co.jp/pc/index_en.html
*The user registration will be needed before connecting to the Wi-Fi.
Free-W-Fi Information/Go Tokyo
https://www.gotokyo.org/jp/tourists/info/wifi.html (Japanese)
You can get the free Wi-Fi card at the airport.
http://flets.com/freewifi/service.html
You can connect to the Wi-Fi at the following famous places.
Nikko Wi-Fi
http://www.city.nikko.lg.jp/seisaku/gyousei/shisei/wi-fi/wi-fi.html
Hakone Wi-Fi
http://www.hakone.or.jp/en/wifi/
Fujisan Free Wi-Fi Project
http://freewifijapan.com/jp.html
You may find other Wi-Fi hotspots except the above places, but due to the security reason, I recommend use the encrypted WiFi hotspots.