Well you hit everything except the World of
Disney store! Here is my suggestions.
Empire State building. You must get there at opening! We were there in December. The line doesn't look long however it was deceiving because the line goes so far & then you can't see anymore past the "next room". We thought we were on a short-ish line but we ended up waiting 2 1/2 hours with 3 kiddies...no pretty. We didn't know where the end of the line was so we had no idea how much longer the wait was...go early!!!!!!!!
Ground Zero is downtown...not walking distance from Times Square (I have walked it but not with the 3 kids) You would need to take a cab...I love NY but I have never (& will not) put my kids on the subway JMHO. Get a yellow cab with a medalion on the hood not a gypsy driver (black town cars & the like) There is no memorial there yet.
The rockerfeller Christmas tree is usually lit the first Tuesday of December however the lights in the stores may be up. The best place to see the windows is at Lord & Taylor. Each year there is a theme to the window displays & they are lovely. L&T is on 39th & 5th. Santa will be at Macy's the day after Thanksgiving. Macy's also has the Percy the Penquin show for kids (corny but the kids like it).
Statue of Liberty/Ellis Island. We have never been as a family but Katie just had a school trip to Ellis Island & Dana chaperoned & they had a great time.
American Girl (our girls home away from home!

) they have been celebrating their birthdays there for 3 years in a row now. Check out there website for show/lunch time & make reservation early especially since its during a busy time...Just to let you know I make my Dec ressies in June/July to be sure of the times/shows I want.
Toys R Us...gets very & I mean very packed right at the time as people are shopping for the holidays. It is worth a trip though. In the front of the store there is a huge-o ferris wheel inside the store the kids can ride. Each car has a theme (barbie, toy story, etc) There is a life size T-Rex in the back that growls & moves. Also a life size barbie house with what else? Barbie merchandise. Haven't been to FAO in a long time since its farther down on 5th towards Central Park (near the Plaza hotel).
Everything on your list looks great & fun..just call for ressies early & get out touring early & you will get to see alot & have a great time!
ETA: If you are looking for a fun restaurant for the kids Planet Hollywood has always provided us with good service, good food, more importantly good coffee!

PH is in Times Square. I do not suggest Hard Rock Cafe (horrible food & worse service) or Mars 2112. Microwaved food & scary servers
Also I checked with Dana & he said Marriott Marquis & the "W" were very nice to stay at

...do not stay at the hotel Edison.