EWR everytime
For Manhatten, EWR is the better option by far.
Shorter queues at immigration, great transport links into Manhatten and when you depart to come home, no horrific taxy times to the runway.
As BA crew, I do a fair amount of JFK flights and last week it took us 1hr50mins to taxy to the runway. This is now the norm, and it will get worse in winter - with de-icing etc.
Enjoy NYC!