Choosing a prepaid SIM card in Japan is slightly tricky. If you need voice calls and SMS, I guess you don't have much choice except SoftBank. However, SoftBank does not have any data plan, so mobile internet usage can be quite expensive on a per-use basis.
If you need only mobile internet but not voice calls or SMS, you then have the choice of going with either b-mobile or e-Connect. For both offerings, you will need to order the prepaid SIM card before your trip and collect it either at the airport or have it delivered to your hotel. Make sure you order it online at least 3 days before your arrival to ensure delivery at your arrival time.
For b-mobile, you pay ¥3980 for the prepaid SIM card and you get 1GB of usage for a period of 14 days effective from the day you start using it. If you need a period longer than 14 days or more than 1GB of usage, you are better off buying a second SIM card rather than reloading value into it due to the hassles involved.
As for e-Connect, you pay ¥4890 for the prepaid SIM card. In this case, you get 1GB usage for a period of 30 days. In their case, reload is strictly not available. If you need more data or longer period, you have to purchase a second SIM card as well.
As my trip was 19 days long, I settled for e-Connect and tried to control the amount of data I use on my mobile device. 1GB isn't alot but it's more affordable to stay within the limits. I felt that anything more would seem to be expensive for a 19 day trip.
Related Guide: http://prepaidwithdata.wikia.com/wiki/Japan