First off, the OP is about LaGuardia, and my OC was about the bus to LGA. You've kinda hijacked this thread to make it about the airtrain to JFK without addressing the bus to LGA.

Second off, your numbers are wrong and don't support your argument.

Your 3.5 million ridership estimate (from Wikipedia) is for 2021 and doesn't take into account the impact of the covid-19 pandemic on travel. According to the Port Authority, "AirTrain JFK handled nearly 21 million passengers in 2019."

Your argument was "JFK airtrain simply don't see a lot of use" and that airports with transit connections "see very little ridership on the transit lines." Regardless of whether ridership is 3 million or 21 millions, that's literally millions of people using transit every year, and between 25-50,000 people each day.

Comparing that number to the number of air passengers is a totally inapt comparison. For one thing, that does not take into account air passengers who use JFK as a layover, nor does it take into account how people travel. For example, a family needs to buy flight tickets for children who can ride the MTA for free. Further, not everyone who flies in and out of JFK is coming to or leaving NYC; people from Long Island are probably less likely to use the airtrain, especially if they don't live near the LIRR.

In any event, comparing transit ridership to air passengers would, at most, support a different argument: that transit isn't the primary means of transportation for air passengers, not that it isn't a popular mode.