I'd guess a PoD sometime during the 60s and 70s would make for an interesting TL. I know that the planning/construction around that period came to a halt thanks to the city's mid-70s fiscal crisis. But at the same time, there were transit projects going on elsewhere in the country that did manage to open. BART opened in '72, DC's metro in '76, and Atlanta's MARTA in '79. Of course, there are always gonna be particular difficulties to building New York transit, especially in the post-WWII era of nationwide car-centric development. But it could happen.
Okay, pretty much speaking post-WWII, you had two main PoDs as far as I can see, and I'll do some brief descriptions:
1) You have a higher initial bond measure in 1950 to pay for the construction of the Second Avenue Subway
or a lack of a Korean War to reduce the construction wars. It is rather unlikely they'd complete the entirety of the Second Avenue Subway either way (but probably stronger with the former I feel), and I'd expect the portion north of 61st Street to the IRT Pelham Line to be built first, with the Pelham Line being shifted to B-Division cars for the SAS like originally planned. I'd expect work to slowly be proceeding downtown, and likely focused on the creation of Chrystie Street Connection in it's original format as proposed for the 1950 Bond Measure.
2) Orient a modified Second Avenue Subway to be built as part of the Program for Action; shift it so that the Phase I built north of 63rd Street sees more of a higher focus in construction. This would also likely require a better plan in increasing the count of stations,
but to develop the construction plan in all likelihood for an eventual expansion to four tracks (this would likely be something similar to what was planned for the BMT 4th Avenue Line south of 59th Street). Getting the initial portion done north of 63rd Street would help, and then likely working down south later on in the 80s or 90s once the portion north of 63rd Street is built. Possibly, you see the portion south of 63rd Street built in a proposed fashion like north with the capacity to build four tracks in the future,
OR, you see significant efforts to make it four tracks alongside a construction of the Queens Boulevard Line superexpress tracks. It
might then be completed by the end of the century, depending upon when the project is started.