The ferry to Statue of Liberty leaves from Liberty Park - a five/ten minute ride from Liberty Harbor marina/cg. It also stops at Ellis Island.
You have two options to go into Manhattan. You can walk up Marin Boulevard several blocks to the Grove Street PATH station. This will take you to wither 34th Street MTA hub where you can hop to several subway lines, or it will take you to the WTC site.
Or you can catch a water taxi that docks right at the marina. It will take you to the foot of Wall Street on the East River. From there you can enter the subway system or walk the surface street to a lot of stuff. The water taxi is my choice. Being dropped off right at my MH, as opposed to that walk back down Marin after schlepping around NTC all day, if worth the couple of bucks.
Your itinerary seems a little aggressive. I hope you can stick to the schedule. You may wish to consider saving one or two stops for another time, and not rush your stops. But either way I hope you have a ball.
