I have a 3G iPhone and it works, in Japan, as it would anywhere else in the world. The days of Japan and South Korea being seperate from the rest of the world are long gone now that 3G has been adopted world wide (they have been 3G for 8 years, and are now onto 4G). To keep the roaming charges down, I use www.jajah.com to make calls, similar to TruPhone.

I haven't used Boingo because I have found it to be confusing and troublesome to use. I use Hotspot:

http://www.hotspot.ne.jp/en/index.html

Pre paid cards are purchased at any Family Mart through their ATM kiosk.

I find it easier to get working, and the number of locations between providers are more or less the same. No matter where you are there will be something near by. I make a PDF map of their hotspots, copied from their website, and keep it on my phone for easy reference.