Just came across your post. In case you are still searching, here's a very informative link:

http://www.pr-roots.com/census.htm

The site indicates that the last Spanish 1897 census of Puerto Rico is available for the following municipalities:
- Complete Ponce [Ponce Historic Archives & LDS microfilm]
- Complete Hatillo [Archivo General de PR]
- Complete Arecibo [Archivo General de PR]
- Partial Río Piedras [Archivo General de PR]
- San Germán [San German Municipal Archives]

San Juan returns destroyed by fire.