There are supposedly SIM vending machines at the airport, but any big box electronics store (BIC, Yodobashi etc) will have a display dedicated to prepaid SIMs. The sales staff at the phone counter of Yodobashi Camera in Akihabara spoke excellent English, if that helps.
I haven't seen a good prepaid SIM service with an actual phone plan, they're all data-only. Depending on your needs, I'd recommend the service I got from B-mobile and So-net.
If you're going to use a lot of data, I wouldn't recommend So-Net: while they had a decent up-front cost of 5000 yen for 3GB of data good for 180 days, but when I went to recharge the SIM they capped the recharge at 1GB for 3000 yen, which was frustrating.