Let me suggest taking SonarQUbe out of the equation entirely and using a tool like SSLPoke to test the Java distribution that’s starting your SOnarQube server and whether it is able to make the connection to you GitHub Enterprise server with what it has in its trust store.
Likely you’ll need to adjust the truststore of that Java install. This is a common problem when a server SonarQube is trying to reach is using a self-signed certificate.