It depends on your budget, and what you want from a hotel. Just a room for the night, or something a bit more luxurious?
We usually want something clean and comfortable, but not luxurious. We've stayed at the New Yorker (we liked this), the Doubletree on Stone Street (comfortable, but quite small), and the Lexington (ok for the money, but not great). All nice rooms, but not much more.
Our favourite though, when travelling with teens, was the Doubletree in Jersey City, as they had suite rooms, with 2 double beds on one room, and a double sofa bed in the lounge with a door between rooms. Worked really well for us, even with three teenagers with us. We slept in one double bed, DD in the other, and two DS's shared the sofa bed. There was a TV in each room, which was great, as we would wake up before the DS's. It had huge windows with a great view over to Manhattan. Kids loved the warm cookies on check-in. Easy and quick to get to Manhattan on the PATH. Only downside was one bathroom, but we coped, and it was cheaper than getting two rooms.