I've had to do many Eastern seaboard connections to SQ at JFK/EWR (but not from locations that SQ sells a connecting flight so I buy my own). It's never ideal but I always give myself a wide berth for the connection...for JFK I usually fly mid morning to arrive around noon-1pm. Last time I got a day room at the TWA Hotel. If you can change the JBU flight for $75 and have the day to spare, I would do that and just pick up your bags at JFK and recheck them for the SQ flight.