Depends a lot on what routes you fly and in what class you fly. In general the hard product and service are very good on both. I prefer JL seats in both J and F over NH, but that may change with the new NH seats.
You also need to check which airlines fly the routes you are most likely to travel and whether the flights are out of HND or NRT. HND can save you a lot of time.
Also if you're going to be flying a lot in Asia in J, check the aircraft being flown on those routes. Seats range from very good (lie flat on JL) to the total torture barcaloungers on NH.
Finally you probably want to credit your miles to a US carrier - UA for NH and AS or AA for JL. UA made significant changes to their program (good if you fly a lot of expensive tickets.... terrible if not.)
Overall, both airlines are great.
If you provide more info, FTers can probably provide more specific advice.