I don't think there's a central place in Eclipse config where you can specify some flags that should be added when Eclipse generates code for you.
The only way to kind-of achieve what you want is to modify each code templates of "Java > Editor > Templates" and surround them with some flags like "// SONAR-OFF" and "// SONAR-ON", and to configure the Sonar Switch-Off Violations plugin accordingly.
But:
This is quite a pain to modify all those templates (even if you'll do it only once)
This won't work for advanced code generation like for "equals" or "hashCode" method