A tempting idea, but it eventually boils down to accessibility. There is nothing of particular interest at Astoria Boulevard to value directing Airtrain service there, which is why it was suggested to just extend the N past Astoria-Ditmars to LaGuardia back in the day. Willets Point is more feasible granted the area is in the initial stages of major retail and residential development, and it offers more transit opportunities, one of which eventually connects to the N at Queensboro Plaza.
Since the Q will eventually run on a new trunk up Second Avenue, and the W was nixed earlier in the 2010's, there would be no service to Astoria-Ditmars if they branched the N off over the Grand Central Parkway towards LaGuardia, and both Astoria Boulevard and Astoria-Ditmars would have to be abandoned (the former sits directly over the GCP).
Considering it took decades to complete only one phase of the Second Avenue Subway, and over a decade to complete the East Side Access, digging subway (most likely tunnel boring because cut and cover causes the most NIMBY noise these days) would blow budgets out of proportion. Neither the MTA or the Port Authority have been very reliable when it comes to delays and cost overruns.