Yep, multimeter.
Continuity (Ohms) check from the two pins on the connector the blower plugs into back to battery negative or chassis ground will identify which one is which.
That being said, most multi-wire automotive electrical connectors I have encountered have some clip/lug/etc. on it to ensure it can only be plugged into it's mate one way and cannot be plugged in "backwards". Is there a concern that your motor might be wired backwards?