I have the same concern and what I have found is this:
A financial account is foreign when it is located outside of the United States, which includes the following places:
United States, including the District of Columbia;
United States territories and possessions, such as:
- Commonwealth Northern Mariana Islands
- District of Columbia o American Samoa
Guam o Commonwealth of Puerto Rico - United States Virgin Islands
- Trust Territories of the Pacific Islands
Therefore, according to this if you have a bank account in a bank located in Puerto Rico, it counts as a foreign bank account for FBAR purposes.
Source: https://www.irs.gov/pub/irs-utl/IRS_FBAR_Reference_Guide.pdf
