From Penn St you take the NJ Transit train to Newark airport, or the LIRR train to Jamaica where you transfer to the AirTrain which brings you to your desired terminal at JFK.
LaGuardia doesn't have a train option though.
But yeah, taking a car from Newark to Williamburg in the afternoon, I guess you've learned not to do that again. :) NJ Transit is your friend.
LGA: None
JFK: Subway,AirtRain
Compare this with HKG or LHR, it is pathetic.
Just like when you're booking a ticket to/from "London", you don't pick Luton if you really mean Heathrow. If my destination was Williamsburg I would pick LGA if at all possible, otherwise JFK. Picking EWR and having to go across the city is not a good plan to start with.
Also, don't take the subway to/from JFK, take LIRR it's like 40 minutes faster.
Also, people should not be afraid of the connecting M60 bus when taking the subway en route to LaGuardia.