The 1 hour stop in the holding pen is a pain. But it's still J class on a LH flight. PE can be very comfortable, but depending on your travel day, JFK flights are typically packed in PE. I like the privacy that LH J on CX affords, but if the PE cabin is somewhere less that 60% full and the seat next to me is open, I can live with it. But the operative phrase is "live with it" vs. something that can be an enjoyable experience. CX865 JFK-YVR-HKG is a little better that you can stay on the plane. For direct flight, you arrive JFK in the evening. The YVR flight is different in that your arrival is in the morning. While I will typically choose the direct flights out of convenience, the evening arrival in NYC after a 14+ hour flight, where I typically wake up about 2-3 hours before arrival, really puts me in a terrible position with jet lag. Coming back from HKG takes me about 4-5 days before I start feeling right. I'm not convinced that the morning arrival makes it better, but waking up just before arrival and forcing yourself to stay awake as late as possible that day, could reset the body clock a bit faster.
I'd say take the J flight. It will add around 4+ more hours to your travel time with an annoying deplane in YVR, but its definitely a more comfortable experience.