San Diego to NYC layover

My recommendation would be to fly into Newark instead of JFK. United also flies direct from Newark to Dublin. EWR is a far more user-friendly airport than JFK, and it is closer in to Manhattan with easy bus connections. Even if your best option for your NY-Dublin flight is out of JFK, you should definitely look for a flight from SAN to EWR.

Although it's likely be warm/more than comfortably warm, I would pick Boston in August hands down over NYC (and I say this as a huge fan of NYC). August in NYC is just miserable (hot, steamy, packed with tourists, and the heat just gets magnified by the cityscape). You can use the T's Silver line to get to and from Boston's Logan airport (you can look at any airport's webpage and it should give you all the options for traveling to/from). https://www.massport.com/logan-airport/to-and-from-logan/public-transportation/

In both cities, the hotels are quite expensive and both are touristy, but I would pick Boston simply on the hope that it's much less humid and hot in August. Given how expensive both cities are, I'd pick one that was simply more comfortable to be in and navigate at that time of year. I would use booking.com or hotwire.com to choose a hotel (but not this early - you won't get any great deals this far out in the future). I stayed at the Royal Sonesta for work a number of times but I'm not sure what your budget is or what style of hotel you prefer - there are lots of choices of high-end business hotels - I'm weary of recommending a business hotel for a leisure trip. Anywhere off the T (Boston's subway) would make it easy to get around.

I disagree about EWR and about Boston being all that much better than NYC in summer.

If I were you I'd stay at a hotel right near JFK and "commute" into the city to sightsee. This would save you wrangling luggage and give you peace of mind that in case some traffic nightmare occurs, you are right by the airport. The hotels near the airport tend to be more affordable than in Manhattan (that is, you could probably find a cheap place in Manhattan but it could turn out to be a real fleabag in a dicey neighborhood). JFK has monorail service that connects to the Long Island RR and the subway system, but with luggage it would be hassle. http://www.panynj.gov/airports/jfk-airtrain.html
I would take a cab or car service.

Having only 2 days, you'll want to map out your top priority things to see & do in Manhattan. First time I went to NYC I was under the impression it was such a small island I could walk everywhere, but that's definitely not the case.

Thank you for the suggestions. I just opted for a stop to the east coast and to take a few days off the plane before heading out again to Dublin. I can now research with a better understanding of the area and the use of the public transportation. This helps a lot.

If you need hotel suggestions in NYC, just send me a PM and I can give you a few. It is definitely possible to cover a certain area or cluster of neighborhoods in NYC (e.g. Lower Manhattan) even in the short time you have. You could do it even without taking the subway provided you really enjoy walking (it will be brutal in August but luckily there are lots of places to duck into for a snack or drink, as well as small parks with shade).

Boston is a great idea. Much smaller and easier to get around for a quick 2 day visit. The Silverline from the airport is easy-peasy and if it unbearably hot you can take a whale watch boat and get out on the water where it will be much cooler. One of my favorite cities - it is small & cozy, very walkable, and has a variety of things to see & do.

I vote NYC although I also love Boston... both could be miserably hot in August.

I would stay in the city if you can and then just walk or take the subway everywhere. We have stayed in Times Square, close to Central park and over on the east side. I would recommend close to the park. I just took a cab into the city and it was a flat fare.