I have this working now. The sonar.sources and sonar.tests properties are defaulted to the sourceSets.main and sourceSets.tests values which are being set by the Java gradle plugin. I overrode both properties to list both java and javascript source directories and started getting the expected results. e.g.
sonarqube {
properties {
property 'sonar.sources', 'src/main/java,src/main/webapp'
property 'sonar.tests', 'src/test/java,src/frontend/test'
}
}