I suspect the C&I office is continually manned throughout the day as there are numerous arriving & departing flights. We were there at lunch time and an officer was present.

I strongly suggest you call. Quoting the CBP website: https://www.cbp.gov/travel/pleasure-boats-private-flyers/pleasure-boat-locations/pr-us-vi

"What information do I need to provide when I call?
The Master of the vessel must report arrival via telephone immediately upon arrival to a designated inspection site within the jurisdiction of Puerto Rico (including Vieques and Culebra) and the US Virgin Islands. See below telephone numbers.
LBO registration number or Float Plan Number (if applicable)
Name, date of birth and citizenship of all persons on board (including passport number and visa information if applicable)*;
Name of the boat and/or boat registration number and nationality
CBP user fee decal number (if vessel is 30 feet or longer);
If qualified foreign vessel, cruising license number
Return contact number

Designated Sites for Inspection at Ports of Entry for Private Boats Operators:

Puerto Rico
The telephone number to report arrival seven days a week is 1-877-529-6840 or (787) 729-6840, manned from 0800 until 2400. After hour arrivals, leave a brief message with boat name, registration number, date and time of arrival and a return telephone number. If no return number or the number is international, please call again after 0800 upon arrival. You will be advised with instructions on entering procedures according to normal hours of the below inspection sites.

U.S. Virgin Islands
Telephone number to report arrival seven days a week are:
St Thomas: 1 877 305-8774
St. John: 1 877 305-8775
St. Croix: 1 340 773-1011 (day time) and 1 340 773-1490 (after business hours)
After hour arrivals, leave a brief message with boat name, registration number, date and time of arrival and a return telephone number. If no return number or the number is international, please call again after 0800 upon arrival. You will be advised with instructions on entering procedures according to normal hours of the below inspection sites.