I do the NYC-MNL trip frequently on both UA and CX, I would not suggest the EWR-HKG flight as it is often late (especially in hot days in the summer) because the aircraft sits at HKG until the next morning, so if there is a problem with a 777 they might swap this aircraft and you get there late and miss the connection. The shortest and best route IMHO is the EWR-NRT-MNL on UA and NH code shared. I have gotten reasonably priced J tickets and also booked Y and used miles to upgrade EWR-NRT. That is a much easier ticket to upgrade than to HKG.