Don't waste your money on Madame Toussau's & Ripleys. They are everywhere & are not uniquely NY.
Pick 1-2 museums; you don't have time to do them all. If you like art go to the Met. If you want dinosaurs go to Natural History.
There's nothing in Flushing Meadows unless you want to go to a sporting event; tickets will not be part of the pass package.
Times Square doesn't have a cost, unless you are paying for a bus to drive you through. Just walk there for free. (think Temple Bar)
The Central Park Zoo is kind of like the Dublin Zoo (Your profile says you are currently in Ireland). It's not huge. If you want a big amazing zoo, go to the Bronx Zoo.
Coney Island is no longer like it was in it's hey day. Take a subway & walk the boardwalk for free. Treat yourself to a Nathan's hot dog & a knish.
For views of the skyline you can go to the Empire State Building or the Top of the Rock. There is no need to do both. For a better view of the city, take a Circle Lines tour.