I did some research, and it looks like the IRT was constructed with a mixture of cut-and-cover and boring[1]. The schist apparently isn't too much of an issue when you have dynamite[2] ;)

[1]: https://mhdh.library.columbia.edu/exhibits/show/irt/laying-t...

[2]: https://www.nypl.org/blog/2015/05/04/subway-construction-the...