Both mine had a preference for a side too, and it was for the side with the biggest supply, which didn't help things...
The key is to keep offering the other side as well since, if you don't BF from that side, your breast will decrease the supply of milk there.
There are different positions you can try to make the baby 'think' he's feeding from the preferred side - the one that worked for us was the 'rugby ball' hold. It's easier if you have a few cushions/a pillow/ a feeding cushion.
There's also some good info on this link
http://www.kellymom.com/bf/concerns/mom/lopsided.htmlxxx