Change your args to be like this:
$meta_query = WC()->query->get_meta_query();
$meta_query[] = array(
'key' => '_featured',
'value' => 'yes'
);
$args = array(
'post_type' => 'product',
'stock' => 1,
'showposts' => 6,
'orderby' => 'date',
'order' => 'DESC',
'meta_query' => $meta_query
);
If you go to wp-content/plugins/woocommerce/includes/class-wc-shortcodes.php (@595) you can find how it’s done for WC shortcodes.