We have 3 kids and have "done Disney Dining" with everything from an 8 month old to a now 8 yr old (our ds are 8 and 7 now; dd is 3). Our favorites, in no specific order: Chef Mickey, Garden Grille, Sci-Fi (our kids think the atmosphere is too cool and were mesmerized -- however, some folk's kids didn't like it), Prime TIme, Teppanyaki (my 8 mos old dd loved this, and so did my boys -- then 4 and 5). The kids enjoyed the view at Coral Reef (but dh and I thought the food was overpriced, even by Disney stds). Pooh is generally well regarded by kids your children's ages -- I would go for Park Fare or Crystal (when my kids were that age, WL had a Pooh Bear b'fast and so did OKW, but that's not there anymore, I don't think). DD loved Storybook B'fast in Norway; not sure, though, what a 3 yr old boy might think! I know MY boys were not inclined to attend! (Princesses! Ewww! Yuck!)
One thing we found is that our kids generally did not eat much at the character b'fasts. If you don't have to pay for them (such as with an infant), it's no big deal. But when you do.... well, DH and I found that b'fast was too important to have them hyped up on atmosphere (and letting $15 pancakes go cold... what can you do with them? And who wants to carry a cold pancake in a doggy bag through the park? Wasted.) So we began doing fewer b'fasts and more lunches or dinners. We ate b'fast in the room (my kids are pretty hungry when they wake up, and it's hard to tell them to "hold it" until we can arrive at a b'fast, unless it's pretty nearby! We also stay in the DVC rooms, so we have a full kitchen -- that helps a LOT.) We find we increasingly get more bang per buck out of the character dinners. I realize someone else posted they thought CM's was gross, but our crew of 8 (BIL and SIL and their 3 yr old) LOVED it. And at dinner, EVERYBODY was hungry, and more inclined to sit and rest instead of being tigger-ish and bouncy! ANother tip -- if you do a buffet meal, try to get an early seating. The food will be fresh and ready, and the wait staff, I think, more accommodating! It has never failed yet for us, in any case!
Hope this helps -- enjoy your trip!