The Witch's lab was the ancient dwelling for the ancient witch, Elizabeth Dexter, and was the location of her heart. It was located in Quadrant KE-12 in Central park. By the time Edward Carnby, Natalie and Boyle went there, an empty building was built on top of it.
It was mentioned by Carnby that the lab had to be in contact with the ground.
The other witch hunters could not be able to sense it, which was why they could not find it.
Many years ago, the witch sacrificed Ward Dexter's daughter-in-law in order to find the occult.
Carnby and Dexter's daughter had to find the lab in order to extract a strand of the heart in order to power up the blade in order to kill the witch.
The entrance to the lab itself was through two mechanical doors. During Carnaby's hallucinations from affected by the dagger's curse, Carnby was able to see the lab.
Carnby and co went through the basement to below the foundations.
Despite the Witch living in ancient times, the fact that the entrance to the lab consisted of modern metallic hatch seemed to be inconsistent with ancient times.