Depending on where you are going in NY, PHL is only 2 hours by train from Penn Station. It'd be less painful than a change and is operated by the 2-4-2 A330. That way you still get pre-clearance too. Unfortunately the 757 to JFK does leave earlier - although that may make it worse from a jetlag perspective - but needs must if it's a short trip.

However I'd definitely do economy out, business back.