Why isn't there a direct train from JFK to Manhattan?

The historical reasons are:

• The rail network was developed between the 1830s and the 1880s, while the airport was not developed until the 1940s. The Rockaway line wasn’t even part of the subway system until the 1950s, a decade after the airport opened.

• When the airport was developed, during the middle of the 20th century, New York City was investing heavily in automobile infrastructure, largely under the influence of Robert Moses, who designed and built most of the city’s expressways, and whose "building of expressways hindered the proposed expansion of the New York City Subway from the 1930s well into the 1960s." That the airport is well connected to the road network, but not the rail network, is no surprise.

• Multiple proposals to connect the airport to the rail network have been considered and for the most part rejected since the 1960s, starting with the Program For Action and leading to the current AirTrain. Reasons for rejection include

  • low ridership projections
  • restricted funding, often because of financial crises
  • opposition from residents of affected neighborhoods

Some quotations from Wikipedia’s AirTrain JFK article:

A railroad link to JFK Airport had been proposed since 1968 as part of the Program for Action, but was not actually implemented for almost three decades. From the 1970s to the early 1990s, various plans surfaced to try to build such a link. Meanwhile, the JFK Express subway service and shuttle buses provided an unpopular transport system to and around JFK. There were 21 failed proposals for rail links to New York City airports during this time.

…

There have been proposals for a railroad link between Manhattan and JFK Airport since 1968, when the Metropolitan Transportation Authority (MTA) proposed an ambitious subway and railroad expansion under the Program for Action. The Program for Action contained a plan to extend the Long Island Rail Road (LIRR) to the airport via the Van Wyck Expressway. … Many Rockaway and central Queens residents wanted the link to run along the disused Rockaway Beach Branch, rather than along the Van Wyck, so that Rockaways residents could simultaneously get express service to Manhattan.

…

Ultimately, most of the lines for the Program for Action were canceled altogether due to the New York City fiscal crisis of 1975.

The article goes on to describe several other proposals, including:

• Bus rapid transit in 1982, "scrapped … in the face of near-unanimous opposition from the communities along the route."
• A direct rail link from Manhattan to La Guardia to JFK in 1990, beset with planning problems and questions about whether its benefits justified its costs, that was scaled down in 1995 to the scope of the current AirTrain.
• A 1999 plan for service from the Second Avenue Subway, through the Montague Street tunnel, to Jamaica via the LIRR Atlantic Branch, where it would join the current AirTrain system for access to the airport. (This plan will have to wait at least until the Second Avenue Subway is complete; it would also require building a new connection from the subway system to the LIRR at Atlantic Terminal.)

In short, it isn’t accurate to say that direct trains to JFK are "not allowed." Everybody agrees that they would be great. The problem is that it has proven impossible to develop a politically acceptable plan to bring that about in a cost-effective manner.

There used to be, in the early 1980s: Wikipedia – JFK Express

It ran more or less along the A train tracks as an express where a single door opened at the stations and you paid an additional fare. At JFK you transferred to a bus shuttle that served the terminals. Tearing up JFK to build a rail line that serves the terminals would be completely impractical.

My memory is that most of the passengers weren’t going to or from JFK, they were commuters from the Howard Beach area who were willing to pay a premium for express service to Manhattan. This together with the cost of running it made it somewhat unpopular politically. Maybe Cynthia Nixon will bring it back?

By the time air travel became economically accessible to the masses, such that high-classed public transportation to airports was on the political radar at all, New York City was already one of the most heavily built-up areas on the planet.

Fitting an entirely new transportation system into Lower Manhattan at that time would have been a non-starter, so the only way to provide a one-seat ride would be to integrate it with one of the transit systems already in place. The options are then LIRR and the subway, both of which were already working under congestion. This would severely limit the service frequency a new JFK line could get without reducing service for existing users of the system.

Since JFK is right next to the built-up area, getting a heavy-rail connection (with the attendant limits on gradients and curve radiuses) into the terminal area would also be difficult, possibly requiring politically troublesome demolitions. A peoplemover allows more flexible routing (and we’ll come back to that). Digging tunnels under the airport might not have been feasible, given the low elevation (and proximity to vulnerable wetlands).

Finally, and possibly the kicker: With a large multi-terminal airport such as JFK, “single-seat train ride to the city center” is kind of an iffy proposition in the first place. You can’t make the trains stop somewhere that is convenient for all the terminals, so many passengers would have to transfer between the train station and their terminals using some other mode. Perhaps a peoplemover, which can more easily snake around between the terminals?

(This is what they have at San Fransisco and Chicago O’Hare, for example: The city transit system does connect to the airport, but then most passengers have to change to a airport-internal peoplemover before they reach their check-in desk. Or, in Europe, consider CDG or London Gatwick).

And what JFK has is exactly that: A peoplemover that connects the individual terminals to the subway and LIRR. Giving one or perhaps two neighboring terminals a subway station would not make it appreciably easier to get to the others than it is today.