We've eaten at Boma several times and finally tried Jiko on our last trip. Sadly, I did not care for Jiko, but Boma is one of my favorites. AKL offers a tour of Jiko and Boma every afternoon. I was talking with one of the chefs at Jiko about the differences between the two restaurants and she told me that Jiko is more French-African influened while Boma is more traditional African food.
As for kids, we ate at Jiko with our 2.5 yo DD. She is used to eating out and was well behaved during the meal. There were many other children eating there, so I think it really depends on your kids. Your 6 yo could go to Simba's clubhouse, but your 2 yo is too young (I think they have to be 4). I wouldn't call either restaurant entertaining, but Boma is a loud, open kitchen environment, so noise is less of an issue.