Black Site is the "grave"/point of origin of The Master. He, himself, doesn't know where it is that's why he wants the Occido Lumen because in its pages the Black Site coordinates are known, though heavily encrypted. The only human who had a chance of figuring it out is now dead, with the professor out of the picture The Master shouldn't have anything to worry about, but like any good ruler The Master leaves nothing to chance.
Little does the Master know the professor passed some of his knowledge on to the ostensibly unread exterminator Vasiliy Fet who has already procured a portable nuke for the destruction of the "Black Site" once its location is revealed in the Lumen.
Hundreds of years ago the site was underwater, off the New York coast within a group of islands known as "Thousand Islands". The Native American name for the island was "Ahsudagu-wah", roughly translated as Dark or Black Place. It's shaped similar to a biohazard symbol.