If you want to extract a preview from a PDF file using the CropBox instead of the whole document, setOption() is the right method:
$handler = new Imagick();
$handler->thumbnailImage(200, 200, true);
It is the equivalent to the -define pdf:use-cropbox=true for the convert command line tool. pdf:use-trimbox is also available.
Note that on my environment the setOption only worked when i called it before the readImage method, which means that you can't pass the filename to the Imagick constructor directly.