About transportation: take the subway, because it is the fastest way to travel from A to B in NYC! There are 7day tickets available. With the Subway you can also go from the center of the City in about an hour to Coney Island.
The Six Flags park you mean is Six Flags Great Adventure, but I don't know how you could go there. Car is possible, but cars in NYC... Traffic jam!
If you love the view of NYC's Skyline, then take a helicopter flight! It is expensive(80$+), but you have a wonderful view over the whole city!!!