Boma's a great choice.
I definitely think you should pay for Kona's lunch OOP, or just drop in for a dessert if it's not busy. You won't regret it. Get the little one a Kiddie Kone - she'll love it! and you can try some of the Kona coffee (it's the best!)
Here's my $0.02 on the three restaurants from the OP.
Kona has fabulous, fresh, creative meals, and some of the best desserts on WDW property. It is my favorite WDW restaurant.
Boma is also great. In addition to the more unusual items, there are always more standard items like prime rib, etc. to choose from- and as was said before, there is a kid's pod with standard picky-kid-pleasing fare.
I would not choose Jiko, as it is a more upscale meal geared to adults, with more exotic menu items and a large wine selection. It just does not seem to be a place best suited for young or picky children.
Choosing between Boma and Kona is tough though, because both are excellent, just different. And both are located in absolutely gorgeous resorts!
Get to Boma early and check out the animals on the Savannah, the fire pit and the beautiful lobby!
Really try to squeeze in Kona, too. It's worth a trip to explore the gorgeous grounds and try the awesome food.