According to Bloomberg[1] construction of the first phase of the second avenue subway cost about 2.5B USD per mile.

At that rate, even if you just look at extending the A/C/E from Jamaica to JFK, you're talking about 15B or so USD. And compared to today's [subway|LIRR] -> airtrain system, you probably only cut about 25% of the travel time (from 60 minutes down to 45 minutes)

Compare that to, for example, the Gateway Tunnel, estimated to cost about 16B USD and double the daily commuter capacity from NJ to NYC (including traffic to and from EWR!), and it's hard to justify new infrastructure to make it easier to get to the airport.

1. In NYC Subway, a Case Study in Runaway Transit Construction Costs - Bloomberg https://share.google/SPcN8iRDZG7lNiwt9

That’s something like $2k/resident to build, and then ongoing maintenance. Seems high for something that most will never use.