Sorry, I disagree with this. The OP is coming from Poughkeepsie, which is an hour and a half north of NYC. They live in the Catskill Mountains. (Think of the movies:
Dirty Dancing and
The Last of the Mohicans where Daniel Day-Lewis was chasing after Madeline Stowe, although both were actually filmed in NC.

) There are some of the most stunning waterfalls, lakes and mountain views up there at the many parks, state parks and open to the public estates in their area. They live within 45 minutes of High Falls, Minnewaska State Park, Awosting Falls, Mohonk mountain, and the Hudson Highlands and can be wonderful, future day trips. When I travel out of NYC for some nature, these places are where I go where my soul sings.
Other than seeing the Alice in Wonderland statue and such, for them to go to Central Park would be such a non-event. As for the CP Zoo, it's little. It would be better to plan another day trip to go to the Bronx Zoo, IMO.
I do agree with you that they have to be mindful of the time it takes to travel from one destination to to another.

As introverts, they can use that time to decompress between sites.
OP, it will take about 20 minutes via the B Train from the Museum of Nat. History to the Top of the Rock.
From there, walk to the 1 Train (south) at 7th Ave and 50th St, (about 8 minutes.) If, before getting on the subway, you first walk to the corner and look down 7th Ave to Times Square, you can spend some minutes marveling at the "2025" sign and pole which the ball drops on NYE. You can even walk down 7th Ave to 47th St, which brings you into the heart of the Times Square
area at Duffy Square. (The
Disney store is there too.

)
Then take the 1 Train, travel down to South Ferry stop which will take about 40 minutes, depending on the time of day, to the Staten Island ferry terminal.
ALTERNATELY: walk one block further west to 8th Ave at 50th St to the E train (south) and take that down to the end, the World Trade Center stop, where the 9/11 memorial is. (Again about a 35 - 40 minute trip.) This may be the better plan, as others have said, it can be an emotionally heavy experience. Then from there, walk over to the 1 Train, ending on a high note, seeing Lady Liberty.
Then you can walk to the 4 or 5 Train to Grand Central to take the train home.
(All these time estimates are if the trains are working and working well and no subway delays, rush hour delays, stalled trains on a track, or "police actions" at a subway station along the line.)
Somewhere along the way, you guys will have to eat. There are four overly priced places in the Museum. The Food Court in the the basement is loud and noisy, especially on the weekends. They may still have "dino burgers" (cheeseburgers,) or dino shaped chicken nuggets. Otherwise, you will have to factor in time for eating elsewhere along the way.