re: NYC with teen daughter

With your limited time, you should plan on only one of skyscraper observation decks. The three of them are the One World Observatory in the Freedom Tower, Top of the Rock at the Rockefeller Center, and the Empire State Building.

If you are already going to do the 9-11 museum, then you will be right at the Freedom Tower, and so I would choose that one instead of making a separate trip across Manhattan to the ESB.

EDIT: Of course, you are also planning to spend time on 5th Ave, where the ESB is. Personally, I like the view from Top of the Rock, as it shows off the ESB and Central Park.