We have visited NYC many times and you could spend weeks visiting stuff and walking miles in the process.
My question would be how much stamina do you have and what’s your budget?
So see the museums. Do the Empire State and Chrysler buildings.
Eat in Little Italy, China town, Katz’s Deli. If you love Pizza do Scott’s Pizza Walk
Hot dogs at Grays Papaya, Burger from Shake Shack.
Times Square, The 911 memorial, Highline Park, Central Park, Grand Central Station,
Do a Broadway Show, ride the Staten Island Ferry, The West Village.
That’s my short list.
I agree the commute does not make sense.
Our best visits were when we would get a room midtown. That lets you get up early , hit the town early in the AM see a lot, take a nap, maybe grab a shower then go back out.