You can pass a properties map to Persistence.createEntityManagerFactory(). To do this you must manage your persistence context yourself (will not be able to inject it).
Another option is to set the property as a Java system property (-D=), this will not override an existing property in the persistence.xml, but with work if the property is not in the persistence.xml.
Another option is to put a SessionCustomizer or a SessionTuner in your persistence.xml to allow your own code to modify the configuration at runtime.