The Chantry of Five Boroughs is actually a misdirection, as much as it is a Chantry, it is also several chantries, satellite chantries changing location and drawing attention away from the one fixed point, the central Chantry in Barnard College. This is where the High Regent of the Chantry of the Five Boroughs conduct his business and the clan is ruled from here. Of course, this location is off limits to anyone that is not a Tremere. Outsiders are handled through the Maupassant Room, a chantry of itself, and a sort of embassy. This is the domain of the Primogen, and that location is known among the Camarilla, though it's status as Chantry isn't. Most people wise enough to tell knows that it isn't the real chantry, and suspect there's at least one other location. Most local Kindred have heard of Barnard College being rumored to be the real one. That there is in actuality five, or even more and that they move locations every now and then is a secret only beholden to loyal Tremere.
Barnard College holds the administration and decisions for the clan are made here. It is a semi-known location, though no outsiders have been let inside.
Maupassant Room is slowly losing it's Chantry status, but remains a meeting point between the insular clan and outsiders, overseen by the Primogen. She in turn struggles to keep it as a Chantry, if for nothing else as a means to a promotion, but the Council of Seven has long considered the structure in New York to be a bit lacking, in adherence to the praxis of the Clan, and has called for a return to more orderly business, now that the Sabbat threat is more or less gone.
There are of course other secrets held by the Tremere, as how they not only managed to keep locations secret, but also managed to move and relocate personell and items without drawing attention, all these years.
The location of the other Satellite chantries are kept a secret, for anyone except those belonging to them or the leadership of the Tremere clan. Even the fact that there's more than one Chantry is a secret.