I am dropping off my D at JFK after spending a night in Manhattan. I will have a car parked in Hoboken NJ. I don’t have to use if there are better ways to get around.
If you’re not going to drive, the best way from midtown is to google map the trip and take the most convenient subway to the air train in Queens which will take you directly to JFK. If your car is in the city, it depends on where you’re going after you drop her off. We often drive from Westchester to Kennedy and it can take from 45-90 minutes to get there. My kids, all of whom live in the city, tend to take the train to JFK unless the flight is very early morning or late at night. Their theory is that with the train, most times you keep moving, even if it takes up to an hour.
Are you trying to get to JFK from Manhattan? You can take the A Train (subway) to Howard Beach ($2.75 one way), then transfer to the AirTran (an additional $5). It’s slow but it will get you there.
A faster, more expensive way using public transportation is to get to Penn Station, then take the LIRR (Long Island Railroad) to Jamaica Station, then take the AirTran from there. The fare of the LIRR will vary if it’s peak or off-peak times (I think a maximum of $17?).
You can also use a taxi or a car service to get to the airport; when I lived in Manhattan I used the car service Carmel. You can reserve it in advance and have them pick you up at a scheduled time and pay in advance.
I would use a taxi or a service. Probably the easiest.
If you’re familiar with the subway system, you can take any number of trains (E from Midtown Manhattan, A or J from Lower Manhattan) to Queens by JFK, then take a separate monorail to the JFK airport. That’s the most direct way. If by car, I usually take one of the Chinese-speaking Uber-like services which is a lot cheaper than Uber, but that probably won’t help you. Taxi is around $50 IIRC.
There’s also always Uber or Lyft…a lot depends on the weather and the time of day.
Train. She can use google maps for the best connections. Taxi/Uber is much more expensive and usually slower.
The flight is at 5 pm. I am worried about the traffic in Manhattan. We could go back to Hoboken and drive. That sounds like it could be faster and less hassle.
Arguably the best way, but certainly not the cheapest-
https://www.godsavethepoints.com/2019/03/26/blade-195-helicopter-transfers-jfk-nyc/
The hassle is driving - I second a car service, and I second Carmel. They’re reliable and easy.
Getting to Hoboken and then driving back will take much more time, more hassle and more risk.
Using the LIRR train from Penn Station or subway and then Airtrain will take you under one hour and there is no risk to get stuck in traffic.
I don’t see any way how going to Hoboken would be an option. You would have to drive back into Manhattan and then have to cross 2 bridges and that would easily take 1.5 hours to JFK in the early afternoon. From Manhattan, you should be able to get to JFK via trains in 1 hour 15 min or so. Or find a car service or shuttle service, which will still take an hour.
Have your D take a subway to Penn Station. At the Penn station buy a train ticket to Jamaica and then take the airtrain to the terminals. This is the best and most hassle free way and I’ve done this 40+ times as you won’t have to worry about traffic. To be safe, take a train at least 2.5 hours before your flight.
We could stay near Penn station and take LIRR to Air Train. Where do you recommend to stay within walking distance from Penn station?
Is she carrying a a larger suitcase - one that will need to be checked in at the airport? Lugging that will make train or subway more difficult. Last time I did this there was a flat taxi fare between JFK and Manhattan - just over $50 if IRC and add on tip and any tolls. I have always taken a taxi, but I am no expert!
I am concerned about getting stuck in the traffic with any car transportation… Is the concern overblown? She can afford any fare except for the helicopter ride 
She is a light traveler. My guess would be a smaller sized (European sized) carry-on.
Uber, about $25 each way
NYC drivers know the best routes around traffic, especially with all the traffic apps available
Traffic is especially light this week due to Spring Breaks & Holidays
I travel a ton for work. For my work trips to NYC (now that I don’t live there any longer) I use JFK and take public transportation. I have a large roller suitcase. As long as the subway station has an elevator (most, but not all do) it’s really not difficult. I am older and very short and not particularly fit.
A nearby hotel would be anything near Madison Square Garden, such as the Hampton Inn Manhattan-Madison Square Garden. But, since Penn Station is accessible via the subway system, you don’t have to stay near there - just travel there from wherever you are.
A taxi would probably end up being $65 one way. My company does profit sharing, so if I keep my business expenses down, it is worth it to me. So I prefer to spend under $10 using the subway/Airtrain, or less than $20 using the LIRR/Airtrain.
I don’t think Uber is going to be anywhere close to $25. Maybe if you use UberPool but that might stop 20 times and it wouldn’t be worth it. The one time I tried Uber in NYC it was from Brooklyn Bensonhurst (much closer to JFK) to JFK and it was $65 using Uber XL or whatever they call the next level up.
Yeah I forgot about LIRR, that’s by far the best. Will take 20 min from Penn Station to Jamaica, then take the Airtrain to JFK. (Or at Jamaica, Uber might be better if you have 2 people since JFK is not far away). Total time around 45 min if you leave around 2pm.
I’ve stayed at the Hotel Pennsylvania for chess tournaments before, so chess rates (you don’t need to play in the tournament) are usually around $160 a night if you book enough in advance.That happens at least twice a year, mid-August and end of December. Probably more often that just those 2 times in a year. Not sure what the regular rates are. It’s a somewhat grand hotel, it’s seen it’s better days, rooms are old and drab, but the location is absolutely right in the middle of so many places, and it’s right across the street from Madison Square Garden and Penn Station.