I'd go with Gatorade. In all reality is any of the two better or worse for you? Maybe not. I always go with something I know is similar in sugar content, but is easy on the stomach and something I could drink while running. I could not drink MD while running but Gatorade I could.
As an aside, there is some evidence that quick fast sugar drinks like these, even Gatorade, aren't really "good" for the body. But if you need quick sugar I don't see a big problem. Is drinking MD once in awhile going to hurt you though? No way.