I went up Top of the Rock on a late Saturday afternoon with my boyfriend and I honestly cannot recommend going up there enough. Everyone says you have to go up there, it's become such a touristy thing to do, but the views really are incredible.
Obviously the other choice is the Empire State Building, which if you are going to do both I would highly recommend going to Top of the Rock in time for sunset and Empire State Building during the day. You definitely get the best view from Top of the Rock and the transition of New York from afternoon to night is magical, all the buildings and skyscrapers look so beautiful with the lights on. It also has the best view if you're looking uptown of Central Park and if you're looking downtown of the Chrysler Building and Empire State.
Also, we bought ourselves the New York Pass which entitles you to free entry to a lot of attractions like Top of the Rock and it allows you to queue jump, so saves you so much time! Would highly recommend purchasing one. If you buy it online, they often have a lot of deals on offer so works out cheaper than if you bought one while you're there.