While the US did conduct a census in Puerto Rico in 1899, the records of individuals were not kept by the US government. The government used those records to determine larger statistics about the population of Puerto Rico. Although individual schedules for the 1899 Census of Puerto Rico do not appear to be extant, the results of this special census were published in the "Report on the Census of Porto Rico, 1899." This publication is available as a PDF on the Census Bureau's website here.
The first available US decennial census for Puerto Rico was taken in 1910. The NARA website links to many online sources for these records: https://www.archives.gov/research/census/online-resources. You may also be interested in the available online records of Puerto Rico that are not US census records, as compiled by FamilySearch and Ancestry:
