SourceSets are indeed a solution to your problem, but I notice you only differentiate your tests by their package names. I'm not sure but that may prove problematic with source sets.
Personally I would prefer a directory structure like this anyway
src
-test
--groovy
---functional
----com etc
---services
----com etc
However, if you are attached to your current structure then take a look at Gradle's test filtering support, which will allow you to filter by package name.
http://www.gradle.org/docs/current/userguide/java_plugin.html#sec:java_test