Rakuten Mobile provide prepaid Japanese SIM cards that can be purchased from their online shop or at a number of retailers across Japan. Rakuten Mobile runs off the NTT DoCoMo LTE network, which has countrywide coverage.
Rakuten SIM cards come in 1GB and 2GB packages, valid for 30- and 90-days and costing around ¥3,219 and ¥4,298 respectively. It is possible to recharge with extra data, in 500 MB, 1GB or 2GB increments. The SIM can be used immediately; all you need to do is configure the APN on your mobile device. You can do this fairly easily using the Rakuten Mobile SIM app (download before you go). Note: Voice calling is not possible with these data SIMs.
Rakuten Mobile also provides SIM cards for long-term use, on contract. Voice calling is an option on contract, if you do not want to go the data-only route.