The "Unofficial Guide" has details on power outlets aboard JAL flights, but yes, at least with the long haul international shell-flat seats, you can use three-prong plugs. I've done that many times on NRT-ORD flights in J. In fact, you can just barely get a MacBook power brick to plug in directly.

Domestically in Japanese households and businesses you'll find that three-prong outlets are less common than in the U.S. though not unknown. Yes, you should probably bring a three-prong to two-prong converter. If you forget to bring one you can buy one without too much difficulty (in Akihabara, for sure).