The only flight from the East Coast to HND is the AA flight from JFK. All of the other flights leave from the West Coast, which adds quite a bit of travel time: 6 hours to fly to SFO or LAX and then about 11 hours from there to HND, versus about 14 hours to fly nonstop from NYC.

Thus flying into NRT and out of HND is probably the best option if you're coming from Newark.