F-irst, make sure you have the TM Attract. During the boss fight, on your first move, press A and attack nothing. Then, when the Boss approaches, use Attract and he will not be able to hurt you. Note: This probably won't work if you are the same gender, and the effect may wear off. If it wears off, use it again.
-If your Pokemon knows Disable and Attract, use them both so the Boss becomes very unlikely to attack. Note: You will have to keep using these when the Boss recovers from them.