Going from North America to PUJ, you're probably not going to get anything nicer (seat, service, IFE) than Continental from EWR. AA, US, DL, or AC from other Northeast cities might be comparable, but IMO CO offers the best option to your destination. You're going to have good legroom, good food, free booze, plus lounge access in EWR.

I'd say don't worry about it too much, for your destination there's not going to be any lie-flats, etc. - just keep ringing the call button for refills and enjoy the honeymoon!