Newark International is really the best place to fly in/out of the NYC metro area. JFK, you have 3 routes, the Van Wyck Expressway, to 95, you will see the new Mets stadium if you go that way, but the darned traffic in that area can be the worst around. The other way out is the Belt parkway to the Verrazano Bridge, or into Manhattan via the Battery Tunnel. From the Belt you'll see the Coney Island section of Brooklyn, also Brighton Beach, Bensonhurst, then Bay Ridge, headed towards the bridge, then you have to cross the Staten Island expressway to get to 95 or the NJ turnpike. If you go to the Battery tunnel you will end up in lower Manhattan, right past the WTC site, and up the west side to either the Holland or Lincoln Tunnel, go all the way up, you will cross the G.W. Bridge, to 95. The last option is to take the streets, to one of the bridges to get across the East river, your choices are one of the main avenues like Flatbush Ave, or Ocean Parkway, head into downtown Brooklyn, to get to the Brooklyn Bridge, Manhattan Bridge, or further north the Williamsburg or 59th st Bridge. If taking the streets, just look at the map and head west, Flatbush ave and others are not in bad neighborhoods, more of a scenic route. You do want to stay on a main avenue, don't stop to ask questions, downtown Brooklyn and surrounding areas are ok, late at night, I do not recommend taking the streets.
Times to travel, if you can be in that rental car mid morning-mid day, traffic will be less, but both the Belt and the Van Wyck can be jammed anytime, so can 95 (Cross Bronx Expressway) you must listen to 1010 wins radio on A.M. for traffic reports.
If you don't want to see NYC, Brooklyn, Queens or Manhattan, the latter being the most desirable, see if you can get a flight into Newark International, and you will avoid traffic problems, anything east of the East River like JFK, LaGuardia, and Long Island can be a real hassle with traffic, the NJ turnpike usually flows well, even in early morning and early afternoon rush hour traffic.
If you head up the Van Wyck, you can also head north via the Whitestone bridge, Hutchinson parkway, to I-684, to I-84, take the latter (I-84) west, eventually over the NYS thruway (I-87), to northern PA, scenic route that way.
I worked in the metro NYC area for 15 years, I know the area like the back of my hand, trust me, whenever possible travel off hours and against traffic, all of which either heads into Manhattan or out of Manhattan, depends on what time of day it is. Saturday and Sunday - early mornings are probably the best time with the least traffic.
