Hi Jacqueline! I've eaten at both Kona Cafe and the Wolfgang Puck Cafe several times with children about the same ages as yours, and they're both good! Did you know that the website
www.allears.net has menus for the Walt Disney World restaurants? You may want to look at the menus for both Kona and Wolfgang Puck to see which one has food that appeals more to your family.
Personally, I would choose Wolfgang Puck Cafe (downstairs) over Kona. My children (and my husband and I!) really enjoy pizza, and the Wolfgang Puck Cafe has wonderful wood-fired pizzas. Also, if you're eating at lots of restaurants in the parks and resorts, your children may find that the offerings on the kids' menu at Kona Cafe are similar to what they've already eaten at other WDW restaurants. At the Wolfgang Puck Cafe, the children's menu features some unique options (including sushi!) that will give them a little variety. The Wolfgang Puck Cafe is a favorite of my family; we eat there on every trip, and we've never had a bad meal. Plus, after dinner, it's fun to stroll around the shops at Downtown Disney.
Hope I've given you some food for thought! Have a great time!