Four of us took the 4:30PM sailing aboard the Clipper City. This was a 90 minute "sail" from Pier 17 near Fulton and South, East of Battery Park. The trip itself goes past the Lower Manhattan Heliport and the South (Staten Island) Ferry Building, proceeds between Ellis and Governor's Islands, and reaches its return point at Liberty Island. From there it heads back through the Eastern side of Governor's Island, comes close to the Brooklyn Bridge, and then docks again at Pier 17. Consider this a leisure cruise up to the Statue of Liberty at a slow pace from which you can enjoy the sights and sounds of the Upper Bay.
They do a 2:30pm and a 4:30pm 90 minute excursion on weekdays, more on weekends. You will need to go to the ticket counter, which is really a small hut-like structure amongst various others between Pier 16 and Pier 17, pay and get your boarding passes there, and proceeded to the end of Pier 17, which you access by going through the mall doors in the middle of the structure to the left of the hut, crossing the building mid-section, and then making a right to the end of the pier when coming out at the other side of the mall. You likely won't see the ship before you go through the mall. If you are using the NY Pass, be sure to go to the ticketing hut first to get your boarding pass. Even though there are tons of reviews stating you have to do this, there were still two people in line to get on the boat who went directly there and were turned back. Note you can reserve your spaces a week in advance whether paying directly or using a NY Pass, and reservations are recommended.
About 10 minutes before departure they will start allowing folks on board. There is no real queue. When they call for boarding, people just line up then. If you want to get a good seat, and if there are a lot of people waiting to get on board, then do be on the lookout for the boarding call. Real seats are limited, are actually benches, and are next to the bar area. There are sitting places all over the rest of the ship which afford better views and more silence, but for those you will sit on regular boat surfaces. Plan accordingly what you are going to wear.
We found the nicer area to be starboard (right) near the boat's stern (end), from which you can get good pictures of the Manhattan skyline as the boat leaves the pier and proceeds to the Statue of Liberty. Since the boat returns from the other side of Governor's Island, the departure is the only time you can get pictures of the skyline up close. Starboard is the best side to see the approach to the Statue of Liberty, and starboard is the side to be to get a better view of the Brooklyn Bridge on the return.
On our particular cruise, there were no heavy drinkers, everyone was calm, the crew was diligent but unobtrusive, and there was not much water traffic. We were able to get up very close to the Statue of Liberty. Although you will be against the sun in the afternoon you can still get some really good pictures. I would expect that on more heavy traffic days the Clipper might not be able to get up as close, but who knows. We had a medium sized cruise ship pass us by, as well as various ferries.
For us, the cost was covered by the NY Pass. If it hadn't, we still would have been happy to pay the $36+ cost per person to take the trip. Remember, it's just a relaxing ride out to Liberty Island, so don't expect a faster ride out around Manhattan or out to Jersey somewhere. Some things to note: there is no commentary other than brief introductory words, the crew expects a tip at the end of the journey although they have no interaction whatsoever with you, there are two bathrooms on board, and the sails are mostly for show (the boat runs on engines the whole way through).
Expect two hours duration between getting your boarding passes and exiting the mall on your return to shore. It's likely the best boating attraction right now in Manhattan, short of a private hire.
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