A large fraction of NYC's subway system was built using cut-and-cover, which is much cheaper than the deep tunneling being used for projects like the Second Avenue line or the East Side Access.
That's before adding other factors such as increase regulation, inflation and good ol' corruption.
That and there was no EPA, no environmental design reviews, not much permitting, lax or zero safety standards (today it is a huge deal when somebody dies on a construction project... no so much back then). There was no ADA accessibility standards, no elevators or required wheelchair access, there was very little underground.
If all the businesses along the block you are trenching through back then went under... so fucking what?
If your 24/7 jackhammers kept all the block up the whole night you’d tell them to take a hike.... etc, etc, etc.
If turns out if you care about any or all of those things, your costs go up. Back then it was all just negative externalities that got foisted on the neighborhoods around them. Think of the negative externalities causes by our interstate highway system. Good luck building that now! It literally divided entire neighborhoods. The entire thing would be require to go into a tunnel under the city. No way would people tolerate that shit now.
While this is all true, on a dollar-for-dollar basis, cut-and-cover is still cheaper than deep tunneling. There's no way around the fact that there is far more expertise, equipment, experience and competition for digging holes compared to digging tunnels.
I really don't understand the aversion to cut and cover these days. Whole blocks of street are routinely closed and resurfaced for long periods of time, especially if sewer work is involved. Businesses in urban environments aren't really reliant on the business from the street parking directly in front of their storefront anyway. Closing a couple blocks at a time wouldn't be all that bad, and it probably wouldn't take too long to throw a temporary grate for car traffic over the open cut anyway.
That's before adding other factors such as increase regulation, inflation and good ol' corruption.