Thanks everyone for your suggestions.
I called and switched to an earlier flight so I now have approx 7 hours for the transfer. This hopefully reduce risk of delays and will give enough time to take the NJ transit train + LIRR as suggested above.
This cost the change fee plus $0.40 difference in fare. I am arriving United (economy) at EWR and departing Turkish Airlines (business) at JFK with precheck and checked luggage.