There is a poorly documented difference between installing neo4j using an installer (which is most common) versus from a zip or tar file.
(A) When you install neo4j using an installer, the installer configures the neo4j server to look for the plugins
folder in the database folder (i.e., under the default.graphdb
folder).
(B) When you install neo4j from a zip or tar file, the neo4j server will look for the plugins
folder in the neo4j installation folder (for example, the plugins
folder should be a sibling of the neo4j bin
folder).
It sounds like (A) applies to you.