If you have a day and want to cover as much ground as you can, here’s a great itinerary:

First, go to Ground Zero (early in the morning is recommended) and St. Paul's Chapel. 

Your next stop is the Statue of Liberty (SOL) and Ellis Island.  To get to the ferry to the SOL/Ellis Island,  go to the 50 Street and Broadway subway stop. Take the number 1 train downtown to the South Ferry stop. Make sure you get on the first five cars of the train because they are the only ones that open at the South Ferry.

Remember that the big wait for the SOL/Ellis Island ferry is security. Make sure you do not have anything on your person (keys? big belt buckles?) that would delay you. Have your tickets in advance, and be ready to stand in line for the security screening long before the time of your boat. If you want to get on the SOL itself (at least as high as they allow these days), you will need to purchase a Monument Tour supplement which is pasrt of the SOL/Ellis Island ferry. This is very popular and you will need to reserve well in advance (in early June 08 there was about an 8 day wait and the next day had early AM and late PM openings).

When you return from SOL/Statue of Liberty, walk to South Street Seaport or take the M15 bus up Water Street or the “free” Downtown Connection shuttle bus (it doesn't run as often as the MTA buses).

 *****AS OF MARCH 18, 2013 ELLIS ISLAND AND SOL ARE STILL CLOSED*****

 

Note:  The original information for this thread came from the   following forum thread: 
http://www.tripadvisor.com/ShowTopic-...