Baseball Reference has now added Japanese baseball statistics going back to 1936. The stats are in a separate section from both MLB and the minor leagues, appropriately cataloging NPB as distinct from both entities. The best part is that the stats are updated daily.
There's still some bugs in the system with how the teams are listed - they seem to be trying to do it by city and getting a little confused about what counts as a city (i.e. Bunkyo isn't a city, it's part of Tokyo). I'm sure they'll get it all settled soon.