From the article it sounds like they actually discovered the leak around 1999 based on a report showing chemicals in the groundwater in 1997.
"According to a 1999 Corps site assessment, the state Department of Natural and Environmental Resources had issued a notice of violation to the Buxton facility in 1997, citing at the time groundwater samples containing chemicals 1,2,3,4 trimethylbenzene and naphthalene.
After discovering that the petroleum storage tanks on the base had apparently leaked, Dokter said, the Corps in the early 2000s removed the tanks and a significant portion of contaminated soil."
I am not sure how they are pegging this to the NAVFAC. It might be because of where the chemicals were found or something. While I was there (Aug 78 - Mar 82) there were at least 2 if not 3 or 4 oil spills offshore. How they decide that this bunch of oil was from the NAVFAC and not from the spills, I don't know.