The answer was doing like this:

        $uploader = new MultipartUploader($s3, $file, [
                'bucket' => $bucket,
                'key'    => $key,
                'before_initiate' => function(\Aws\CommandInterface $command) {
                    $command['StorageClass'] = 'STANDARD_IA';
                }
            ]);

Thanks to Chris Haas!