Great Kills on Staten Island east shore south of VN bridge is good.
Great Kills is my 'usual' when passing through NYC. Its within reasonable proximity to 'stage' for running through the East River to catch the exact change of tide/current at Hell Gate .... and is protected from 'all' directions if the weather is snotty. You can anchor along the NE shore (inside) or pick up a vacant mooring.
The distance from Sandy Hook to Hell Gate makes it more difficult to stage for Hell Gate.