Intermediate image generation is extremely rigid. image_resize() keeps it close to code and completely lacks hooks.
Pretty much only option for this is to hook into wp_generate_attachment_metadata and overwrite WP-generated image with your own (which will need bit of a image_resize() fork).
I need this for work so I might be able to share some code later.
Ok, here is rough, but working example. Note that setting up crop in this way requires understanding of imagecopyresampled().
add_filter('wp_generate_attachment_metadata', 'custom_crop');
function custom_crop($metadata) {
$uploads = wp_upload_dir();
$file = path_join( $uploads['basedir'], $metadata['file'] ); // original image file
list( $year, $month ) = explode( "https://wordpress.stackexchange.com/", $metadata['file'] );
$target = path_join( $uploads['basedir'], "{$year}/{$month}/".$metadata['sizes']['medium']['file'] ); // intermediate size file
$image = imagecreatefromjpeg($file); // original image resource
$image_target = wp_imagecreatetruecolor( 44, 44 ); // blank image to fill
imagecopyresampled($image_target, $image, 0, 0, 25, 15, 44, 44, 170, 170); // crop original
imagejpeg($image_target, $target, apply_filters( 'jpeg_quality', 90, 'image_resize' )); // write cropped to file
return $metadata;
}