When cropping gif-images (I had no problems with jpg and png images), the canvas is not removed. Please run the following command on the cropped gif, to remove the blank space:

$im->setImagePage(0, 0, 0, 0);

Here is a simple function to create a thumbnail. It accepts an additional parameter to set the focus point of the generated thumbnail:

<?php
function thumbnail($image, $new_w, $new_h, $focus = 'center')
{
    $w = $image->getImageWidth();
    $h = $image->getImageHeight();

    if ($w > $h) {
        $resize_w = $w * $new_h / $h;
        $resize_h = $new_h;
    }
    else {
        $resize_w = $new_w;
        $resize_h = $h * $new_w / $w;
    }
    $image->resizeImage($resize_w, $resize_h, Imagick::FILTER_LANCZOS, 0.9);

    switch ($focus) {
        case 'northwest':
            $image->cropImage($new_w, $new_h, 0, 0);
            break;

        case 'center':
            $image->cropImage($new_w, $new_h, ($resize_w - $new_w) / 2, ($resize_h - $new_h) / 2);
            break;

        case 'northeast':
            $image->cropImage($new_w, $new_h, $resize_w - $new_w, 0);
            break;

        case 'southwest':
            $image->cropImage($new_w, $new_h, 0, $resize_h - $new_h);
            break;

        case 'southeast':
            $image->cropImage($new_w, $new_h, $resize_w - $new_w, $resize_h - $new_h);
            break;
    }
}
?>

Actually, the Imagick::setImagePage(0,0,0,0) is also handy with jpgs and pngs, if you plan to do any more changes on the cropped image that involves positioning and/or gravity (I created a script that does crop, face blur and watermarking in one go, and had a hell of a time determining why the blurs and the watermark text never showed up...).

I have a function that takes an image, resize and crop it, and save it as normal, then resize it again and crop it again to create the thumbnail. The numbers of the second crop were WAY off, and the calculations were perfect, the problem, was the second crop wasn't resetting the imagePage, so if you try to crop the same image twice, it will be a good idea to reset it first:
<?php
$thumb = new Imagick($file)
$thumb->resizeImage($r_w1,$r_h1,Imagick::FILTER_CATROM,0.9, false);
$thumb->cropImage($w1,$h1,$l1,$t1);
$thumb->writeImage($destinationPath.'/'.$fileName);

$thumb->resizeImage($r_w2,$r_h2,Imagick::FILTER_CATROM,0.9, false);
$thumb->setImagePage(0, 0, 0, 0);
$thumb->cropImage($w2,$h2,$l2,$t2);
$thumb->writeImage($destinationPath.'/'.$fileNameThumb);

?>

BTW, i needed perfect dimentions so i had to set the "bestfit" to false.