The Health and Human Services(HHS) Secretary can make that determination in conjunction with the CDC. From the CDC website
Under section 361 of the Public Health Service Act (42 U.S. Code § 264), the U.S. Secretary of Health and Human Services is authorized to take measures to prevent the entry and spread of communicable diseases from foreign countries into the United States and between states.
The authority for carrying out these functions on a daily basis has been delegated to the Centers for Disease Control and Prevention (CDC).
Under 42 Code of Federal Regulations parts 70 and 71, CDC is authorized to detain, medically examine, and release persons arriving into the United States and traveling between states who are suspected of carrying these communicable diseases.
As part of its federal authority, CDC routinely monitors persons arriving at U.S. land border crossings and passengers and crew arriving at U.S. ports of entry for signs or symptoms of communicable diseases.
When alerted about an ill passenger or crew member by the pilot of a plane or captain of a ship, CDC may detain passengers and crew as necessary to investigate whether the cause of the illness on board is a communicable disease.
In other words, the CDC can already detain you if they think you have a communicable disease and are flying into the US.