Jetstar Japan (JAL's low cost short haul arm) does as mentioned fly from NRT to Okinawa. They fly from T3, which is walkable from T2 where JAL arrives. There may be other low cost carriers doing the route as well.
ANA domestic departs from T1 South Wing, and you'd need the free shuttle bus to get over there.
3h 25m should be fine for making the connection. Though of course, in case of a massive disruption your connection is not protected.