I think we can get decently close with a half-system closure setup. Increase service significantly on half the trunks in Manhattan, and then use night buses to cover the gaps in the outer boroughs: 1drv.ms/w/c/566715f8...
The Berlin model works really well -- run night buses that ~exactly replace the rail service on Sun-Thu nights and run the trains 24-hours on weekends.
Harder to follow the NYC subway lines exactly over the river crossings, though.
