You can check for subway construction and changes at www.mta.info - they should have that listed in advance.
If you stay at one of those hotels and the A train is running, it really may not take you much longer than a cab/Uber/Lyft depending on traffic, and it will obviously save you quite a bit of money. Obviously, you'll want to see if you have all your suitcases as that could make it less convenient to take the subway especially with a toddler.
NYC subway cars are air-conditioned. The platforms are not.
Staying at either of those is also a good option, I think, because you have good parks nearby and can spend some time outside with your 2-year-old. You even have the carousel down in Brooklyn Bridge Park overlooking Manhattan. Also a lot more food options now than a few years ago in the Financial District (on weekends).