new ProcessBuilder("cmd", "/c", "cls").inheritIO().start().waitFor();
Solved here: Java: Clear the console
I realize this is an old post, but I hate when I find questions with responses of never mind i got it, or it just dies off. Hopefully it helps someone as it did for me.
Keep in mind it won't work in eclipse, but will in the regular console. take it a step further with if you're worried about cross OS:
final String os = System.getProperty("os.name");
if (os.contains("Windows"))
new ProcessBuilder("cmd", "/c", "cls").inheritIO().start().waitFor();
else
Runtime.getRuntime().exec("clear");