President Eden makes clear pre-war bunker complexes evacuated to the West-Coast years after the war.
President Richardson makes clear that the Oil Rig and Navarro willing be getting the Curling-13 vaccine so that they were not affected by the completion of the Project, ergo those are the two primary locations of the Enclave otherwise he would have mentioned others or wouldn't have been so specific.
There are no Enclave hiding anywhere else, to be in the Enclave you have to be from the Oil Rig to have been apart of their society. Say there was some bunker that was full of other descendants of the US government, they wouldn't be automatically be part of the Enclave would they? They'd have their own society and culture and beliefs completely separate to the Enclave.