I've had this happen before, and let me tell you, it thoroughly pissed me off!
For one, my feelings are that children will be children... they're going to "be loud", jump around, try to talk to people in the next booth, and crawl under the table to switch sides every five seconds. I've never been bothered by other children doing this, so it completely floored me the one time that someone told me to "keep control of your kid" because my daughter had been bouncing around in the booth next to me.
I have a temper, so I probably handled it wrong - I told the guy that if he wanted to eat at quiet place, he should have stayed home. Public is public, and I'm not going to hide my child for, quite simply, being a child! I would have understood if she had been screaming and throwing a kicking fit - but complaining that she was moving around too much just struck me as extremely rude. If she was bothering him, he could have politely told us, and we would have asked the server to box up our food.
If I hadn't been so ticked off, I would probably have said something like, "I am sorry that you were inconvienced." I wouldn't appologize for my child's behavior, since there was nothing wrong with it, but to be polite I would have appologized for something... in this case, that the other person felt that there was a problem.
Congradulations on not ripping his head off! LoL.