Best of NYC goes around Manhattan island and is a day time tour. Landmarks cruise which only covers southern half of Manhattan from Pier 86 to the Brooklyn bridge and back, also a daytime tour. Liberty tour I believe covers only the Liberty Island and Statue of Liberty, also during the day. Harbour Lights is a romantic cruise covering the same route as Landmarks cruise but at night time when the city is lit up.
Circle line is a great inexpensivei cruise which completely encircles Manhattan island. I grew up and the area and i believe it's one the best.
The main difference is the time of the cruise Harbor life is a night time cruise that allow you to see the city at night
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