Change the ordering of shipping methods
Since the introduction of shipping zones. Default shipping method ordering mechanism has been removed.
You can still alter the ordering by navigating to:
Wordpress admin -> WooCommerce -> Settings -> Products -> Shipping methods order
Drag and drop shipping methods the way you like and save.
If the new order does not appear, enable temporarily Shipping debug mode.
WooCommerce -> System Status -> Tools -> Shipping Debug mode
http://jeroensormani.com/shipping-debug-mode/