The Ground Zero TFR has expired ... there was a TFR around the Statue of Liberty around July 4th but it may also have lapsed ... check to be sure.
Yes, you can proceed VFR over JFK as long as you're outside (above) the Class B. That said, I would strongly advise either filing IFR or seeking flight following, just to cover yourself.
New York Approach usually won't approve routings over LGA ... the best routing to overfly NY airspace is V16 ... Coyle to JFK to Deer Park to Calverton to Norwich. ATC grants that routing to overflights routinely.
In fact, depending on which Boston airport you're going to, IFR arrivals are often routed over Norwich, via the Woons arrival.
If you have life vests, another easy routing is Sea Isle, V139 to Hampton ... you're about 30 miles offshore at the furthest point.
Good luck and fly safe!
R