Let me preface this by saying I don't think this will ever happen.
That said, any subway extension in Queens or anywhere else in the five boroughs would be paid for by different stakeholders. 2nd Av was US/NYS/NYC; the 7 was wholly paid for by NYC. There are definitely expansion needs NYC needs more.
For this project, much more benefit could be gained by through running NJT-LIRR rather than building new tunnels and a subway extension. They just need a dual mode AC/DC (hums "Hells Bells" to himself while typing) that could run out onto Long Island. It's less than 5 miles from Penn to Woodside; I'm sure it's even less from where the NEC diverges. You could string catenary to Woodside for the extra couple of miles, use it as a transfer station to the LIRR, and turn trains there.
Otherwise, this sounds like a PATH project to me. PATH is overseeing the Gateway tunnels; I think up-thread I said something about making those tunnels two level similar to the East River tunnels used for both Subway and East Side access. Let them run a line from Secaucus and/or Newark and maybe dust off that deep cavern station plan for Macy's basement LOL.
NJT could already through run to Westchester and Connecticut (where there's an obvious need for reverse commuters) that wouldn't involve tying up additional slots for MNRR's Penn Access.
Sounds like I"m heading over to the Penn Trackwork thread