It should be built below ground level, as deep as possible, and the subways should all be rerouted to go right by it. Not through it, like the world trade center, but beside it. Make sure their sleep is just as punishing as being without sunlight
Building below ground would probably more than double the cost. You have to dig, possibly blast (in the city) the dirt. You’d have to move the dirt somewhere else. You’d have to not only waterproof the structure, but you’d need special equipment running 24/7 to dehumidify the air. Probably the crew and worker types you’d need for the dig phase are not the same as the ones you’d use to build the structure and you’d have to find them somewhere as they probably don’t live and work nearby. I’m sure there are other issues I haven’t listed.