I have not personally experienced them, but just from being familiar with the neighborhoods, I'd probably pick the Edge (unless someone is afraid of heights, because that thing looks terrifying to me!). From what I've read you can see the cool midtown landmarks like the Empire State Building and the Chrysler Building, and it's fairly close to them. Plus you can see pretty much everything else - the river views, downtown, etc.
The WTC is miles downtown, in the financial district, so you would have a distant view of the more historic buildings. You can see the Statue of Liberty from there, but it's pretty far away and you're already going there so you'll see it up close. The Empire State Building is cool to visit, but do you most want to see it from the inside or the outside?
(I do feel obligated to comment that there are some great ways to get skyline views that do not involve paying $100 for your family to go to a touristy observatory, like the parks along the East River in Brooklyn near the Williamsburg and Brooklyn bridges, ferry rides, etc.)