A highlight from our New York trip was a visit to the Top of the Rock, which easily has the best views of Manhattan. I've been up both the Rockefeller Centre and Empire State Building before, and the Rockefeller is by far my favourite. My main reason for preferring it is the queues were a lot smaller both times I've been, but you have the added bonus of having the Empire State in all of your photos from the observatory. You're also a lot closer to Central Park and get a much better view of upper Manhattan.
Next time I go back I will definitely be going up both buildings, the Empire State is so iconic and worth every dollar.