I mentioned some of the Japan-specific issues here:
http://www.flyertalk.com/forum/trave...on-asia-2.html
I have usually used JCR Corp based in Hawaii for my visits as they will ship the kit to your home before you even leave but there are several companies in the market.
http://www.jcrcorp.com/
They will rent 3G/4G SIMs from DoCoMo (in JCR's case) that work with any WCDMA2100-capable device. As I mentioned, my Nokia supported this 10+ years ago and these days basically any Android will.
The Cell/SIM rentals will express-ship the equipment to your home before departure, or preferably to a Japanese hotel or address. When you're leaving, just pop the gear into their prepaid mailer and drop it at Japan Post or a courier. If you've never been, the hotshot/overnight courier networks in Japan are AMAZING. Just look up 'Airport Takkyubin' for the greatest idea EVER..
Basically, if you're a light data/phone user and visiting for 7 days or less, stick to the prepaid SIMs. If you'll be surfing, translating, mapping or visiting for 2 weeks or more, order a SIM from the rental agencies; it will cost a bit more but also be *unlimited* usage- no recharging, no buying, no installing and translating and flat rate. ^