Downtown Alliance: Hit the historical hotspots of downtown Manhattan with this comprehensive tour.
Subways and Buses: Travels around Manhattan and the other boroughs of the city is easy and convienent. You can check subway lines and bus routes by visiting the MTA website. 
Staten Island Ferry: Most travelers take the Staten Island Ferry to NYC. Parking is easy, (currently $7.00 all day) and safe. A shuttle van will take you to and from the ferry. The ferry operates all day, seven days a week including holidays however schedules do change.
NY Waterways: another option to travel from New Jersey to NYC is the NY Waterways Ferry. This is a great option from Weehawken NJ and allows you bus access to various NYC attractions.