Their site states that you need to book in person with a city pass at their location at Pier 55. When we went, we were able to get on the next cruise so we didn't have to wait long, but we had planned to visit the aquarium first if we couldn't get a cruise until later in the day.
I would call them.
I used CityPass and they told me to just be in line early for the tour that I wanted to go on to ensure the boat didn't fill up.
I would call them directly if they do not have options on their website
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