Ellis Island impressed me the most (love that scene in The Godfather II when young Vito is quarantained there), never went to Liberty island, figured there wasn't much to see there except for the statue.
Make sure you get your show tickets at the tkts booth on Times Square (46th street/broadway I think), last minute (and 50% off!) is just so much better!
Walk your way down from Central Park to Ground Zero (Trax I can't believe you said to put Ground Zero on the bottom of the list! The photos that have been put up there are amazing), there is so much to see, so may different areas etc.
Make sure you get some restaurant/club recommendations before you go, and don't wind up at Bubba Gump's
.