Here is a problem/issue found while using Sonar in a Maven 3 Java JS project using JENKINS
If you want dependency analysis then indeed the only way it to use Maven plugin to do analysis.
If you want to be able to override default Maven source directories using the property sonar.sources from command line then you should watch/vote for this ticket: https://jira.codehaus.org/browse/MSONAR-70
Note that starting from SonarQube Maven Plugin 2.3 we are using internally sonar-runner API so overriding properties from command line may work in your situation (as it seems you have a single module project). But no guaranty until MSONAR-70 is properly fixed.