Don't do City Pass or New York Pass or any of the other combination deals as you won't have time to visit the other attractions.
Top of the Rock is in the heart of Midtown and in my opinion has the best view. (but I am biased)
Not sure if one of your kids is a young girl bur the American Girl store and
Lego are right in Rockefeller Center.
As far as waiting online goes, tickets are all timed. You can purchase up to a year in advance at topoftherocknyc.com
Enjoy the view and enjoy the cruise
Edited to add the view