Just thought I'd chime in like others. I live in VA and have only been to NY about 10 times in the last 5 years. I've done a few things suggested and agree with what most people have "said".
My DD(9) and myself (43) are heading up to NY this Monday June 3.
We do it a little different. We use Priceline and stay in NJ. Usually Secaucus-North Bergen section. It has bus service (320) right outside the hotel's If we get the Holiday Inn, Hyatt or Courtyard. We have gotten the Sheraton that used the water taxi.
I checked this morning and wasn't able to get a room and didn't use express deal. I'm not picky on the room as long as it's 2.5 stars or up. We usually get the room for $80 a night with free parking. (The Sheraton in Weehoben charged $20 a day.) Not sure what you are paying, but you might look into the Sheraton . The rooms in NY are small compared to what you'll get in NY (what I've read)
Top of the Rock is so much better, shorter lines, less expensive, cool elevator ride up, amazing view.
We have done Empire and lucked up on short lines but I've never been back. I've went back with friends and did TOtR.
Dylans didn't really wow me. This trip we will do what was suggested like you and hit economy candy.
We'll do a Yankees game. (day of the game at Model's 42st you can get half price tickets. I'm no big fan, but It's a fun time and beautiful stadium.
We've seen Mary Poppins and Wicked. Both were great. Bronx zoo was ok, but it's just a zoo.
Whenever we've seen the Statue of Liberty, we've just caught the free Stanton ferry, but it sounds like it might be harder to go.
Chinatown, we get foot massage, she gets her nails done, there is a ice cream place in chinatown that's "famous" and then the bakery in Little Italy that is mentioned.
Try "lobster tails" at the bakery. (Or if you go to Carlo's bakery in Hoboken on your way home. you can pre order and pick up behind the store. you don't have to wait in line. just call in your order)
Coney Island was a dump, but we enjoyed our Nathan's hot dog!! And we rode the big ferris wheel thing.
We do the American girl store, central park, toys r us (cool store with a ferris wheel inside) MTV sometimes has a crowd downstairs when somebody is in the studio.
I've had friends get tickets for david letterman the day of the show, 2 went 2 of us hopped the subway and went to the Village.
There's the famous pizza place near 42 street (john's or something. i think it was a church?)
It's NY, hustle bustle noise, excitement, people yelling, horns blowing, rude cops, beautiful people, street vendors,
Just have fun and plan on coming back.