Do the open top bus tour. We did the red bus tour, and it offered 4 different routes, or loops as they call them, for 2 days unlimited travel for $49. They covered Uptown, Downtown, Brooklyn, and the Night Loop (which is a combination of the other three, which only runs at night).
They are also "hop on, hop off" so they not only enable you to see all the attractions, but they stop at each on so that you can get off eg at the Empire State, go up it, come back down and hop back on the next bus that comes along (approx every 10 minutes)
We thought this was an excellent way of seeing all the sights, and on the second day we mostly just used the buses for transport as we had done most of the sights, and found that one of their buses stopped right beside our hotel so we were able to use it to get to Times Sq as well as using the Night Loop to get home!