Hi, we added extra hotels to our package its up to you. We also paid for our taxi from JFK to Manhattan (about £20.00) and then had to pay for our taxi to Brooklyn Pier.
If you book a cruise only you can add whatever you like onto your cruise. If you've booked a cruise & flight package your travel agent should be able to move the flight to suit your requirements.
You don't have to use the cruise line option you can book your own hotel but getting to it from the ship and then onto the airport is your problem, but it can be done.
We booked cruise only on QM2 to New York (June 2) & booked independently (on net)the Milford Plaza Hotel (3 star standard) just one block away from Times Square & theatres of Broadway - good loction for tour busses & restaurants or diners too. Yellow cabs were plentiful from dockside & we waited 10 mins in a queue to get one. The fare was 26 dollars for the 25 min ride, much cheaper than booking through Cunard!