I agree with the suggestion for JFK- Take the LIRR (Long Island Railroad) to Jamaica). It is a 20 minute ride from Penn Station to the Air Train and you just have to go up 1 flight. The LIRR runs frequently, is comfortable and has luggage racks.
For LGA- any major subway stop in queens is a hassle for getting an Uber. When I go to LGA and the Q70 bus is messed up. I take a green NYC metered taxi. They are always plentiful at the 74th st/Roosevelt Avenue stop.