We had New York CityPasses which included a Landmark Tour via Circle Line (1.5 hours) or Ellis Island. Since the latter was far cheaper, we decided to get tickets for the Circle Line cruise and upgrade to the complete Manhattan tour (also called Best of NYC) for an extra $5 each. We went to the pier a few days ahead of the day we wanted to travel to get tickets, which was worth doing as we had to queue for about 25 minutes to exchange our CityPasses for tickets.
On the day we turned up about an hour early and people were already queueing to get onto the boat - I'd say there were at least 50 people ahead of us. It's worth noting that the nearest subway stop to the pier is Port Authority Bus Terminal/42nd Street, which is a 10-15 minute walk away, so do factor this into your time getting there (or get a bus from 42nd St). The queue isn't particularly well managed - no cordons or anything - and the priority guests who paid more for a premium area had to be squeezed past the rest of us.
We boarded about half an hour before the cruise was scheduled to depart and quickly found seats on the upper deck (outside) on the port side. General note that this side is better because the boat travels anticlockwise around Manhattan so you will have better, less obstructed views on the port side. Seats are comfortable and plentiful. Our cruise was nowhere near full, and since the weather was good, most people were on the upper deck. There are hundreds of seats inside, on two decks, and they were almost completely empty, except for the premium seating area. There is a small bar on the outside deck and a larger bar downstairs which offers hot food. Plenty of restrooms on the lower deck.
As a sidenote, if the cruise is likely to be fully booked and you don't have time to queue in advance, the premium area is probably worthwhile. If you are able to queue up an hour or so before departure and want to be outside, I wouldn't bother with the premium seating. It's a small, cordoned off area inside, so you don't necessarily get to be by the window, you have to look through a window rather than being outside and while the seats may be a bit more comfortable, the normal seats aren't uncomfortable. I wouldn't pay an extra $30 for this.
Anyway, back to the main cruise. We set off promptly at 1.30pm and luckily were able to travel all the way around the island. It is really important to check tide times before you book, because if tides are high when you are cruising, you will NOT be able to travel all the way round the island because the boat will not be able to clear the bridges.
The views from the boat are spectacular. Not only do you get to see the main sights from a different perspective (Empire State, One World Trade Center, Statue of Liberty, Brooklyn Bridge, GWB etc), you also get to see the bits of Manhattan that you might not otherwise see - the beautiful leafy bits, the Bronx, etc. Our tour guide was fantastic - very informative, with just the right hint of humour.
I think we were lucky in that the cruise wasn't packed to the rafters. There was plenty of space to walk around, and the opportunity to go out onto the bow and take photos was fantastic, particularly passing the Statue of Liberty where we got great views, and the boat turned around so that both sides were able to take unobstructed photos.
I highly recommend this cruise. It's an amazing way to see Manhattan. The guide is great, the amenities on board are fantastic and if you're able to line up early, you will get a great seat (port, remember!) and beautiful views.