Well since the OP has a home airport of Austin TX, I will assume that a starting point in the USA is his preference.
As JL don't have Y+ availability USA<->Japan, I would say it depends on 2 things.
1. Do you have the miles and $$ for an upgrade of AA metal to NRT
2. In straight economy which is the cheaper routing? via NRT or via HKG
Note that you would probably want the AA code shares in both cases....
Or your mileage earning would be limited
Happy wandering
Fred