Bring the Firefox Browser to Front using selenium Java (Mac OSX)

Store the window handle first in a variable, and then use it to go back to the window later on.

//Store the current window handle
String currentWindowHandle = this.webDriver.getWindowHandle();

//run your javascript and alert code
((JavascriptExecutor)this.webDriver).executeScript("alert('Test')"); 
this.webDriver.switchTo().alert().accept();

//Switch back to to the window using the handle saved earlier
this.webDriver.switchTo().window(currentWindowHandle);

Additionally, you can try to maximise the window after switching to it, which should also activate it.

this.webDriver.manage().window().maximize();