If schedule is a factor, then keep in mind that the CX flight from JFK to HKG is over 20.5 hours in duration because it has to stopover in YVR. Add in the transit and flight time to Japan, and you are looking at over 24 hours of travel time.

But if time is of no importance, then I would go with CX. In fact, the extra flight time could be to your advantage since you will get to enjoy more of the inflight service. Also, you would be able to visit some incredible lounges like the BA Terraces at JFK and of course, CX's Wing and my favorite, the Pier, both at HKG. Though I'm sure the lounge at NRT would be excellent since that's JL's primary hub, I am unqualified to speak of the Sakura Lounge at JFK.