Hi,
My nephew has a very hard time sitting in restaurants. We discovered when we went out for dim sum on my birthday, that he loves loves loves going out for dim sum. You can see all the food choices, pick small amounts of different items, and the food arrives instantly when you walk in. Chau Chow City in Chinatown (or the one in Dorchester, which has parking) is great for this.
My daughter is younger so I've only heard this secondhand, but some Bertuccis will give the child a piece of dough to play with. Depending on your child's temperment, this could buy you some time.
If you're not a fan of fast food or chain restaurants and your kids are in preschool or day care, you might ask the other parents where they like to take their children. Maybe they have some local hidden kid-friendly gems to offer.
If you're in Arlington, there's a little cafe or diner, the name of which escapes me, near the intersection of Mass Ave and Park Ave that is filled with toys and kid-loving waitresses.
If you're not too far away from Cambridge, as someone already mentioned, Full Moon is great for kids who cannot sit still and the food is excellent.
Best of luck!