Central Park Zoo (weather dependent) is good for a kid that age because it's in the middle of Manhattan (less travel time) and it's a very confined loop, so by the time your kid has entirely lost interest and/or is melting down, you are done and can get back to your hotel quickly. The usual suggestion for kids would be American Museum of Natural History. I don't think you will make it long with a 2 year old, so just be ready to miss quite a bit.
I have an almost two year old, but I live in the west village downtown so all of my other suggestions are tied to the west side of lower Manhattan.
In that area, assuming weather is nice and you are sufficiently dressed, you could stroll your kid around the Little Island and then, when they get antsy, take them a 10 minute walk down to the playground at Pier 51. This is also close to the Chelsea Market (indoors and stroller friendly) and Whitney Museum (indoors and stroller friendly, but obviously depends on your kid's tolerance for adult stuff - maybe Pier 51 after Whitney). The lowest High Line entrance is also right there and is stroller friendly.
There are a surprising number of good restaurants that are kid friendly in the 5:00-7:00 dinner window. Meaning, they have high chairs and won't treat you like a pariah. Don't expect a Texas-style kids menu, but if you want actual good food and not shit food in midtown, suggestions include: (1) Barbuto (we eat here once a week at least); (2) Pastis; (3) Anton's; and (4) Locanda Verde, which is farther downtown in TriBeca. All of those are also good lunch options. Pretty sure Locanda Verde does a Thanksgiving lunch if that is something you need. I have plenty of other suggestions (again, mostly in the West Village and TriBeCa), just PM me if you need more help.
Breweries are also great for kids and adults, but all of those are in Brooklyn. If you want to venture that way, I can give suggestions.