Hi, Janet! I know with my girls, asking this question is going to get me three different answers! It really depends on what your children are interested in and what they like to do.
I think, hands down, the best theme park for this age group is the Magic Kingdom - although I think the Magic Kingdom is the best theme park anywhere, for anyone! For kids, the Magic Kingdom offers fun, fantasy, and a whole lot of pixie dust! There are many rides and attractions that are geared to appeal to people of all ages, and it's the park where I know I can take my girls, ages 17, 8, and 3, and know that not only will they all have a good time, we don't have to split up for them each to have fun!
My three year old absolutely loves Animal Kingdom. She truly enjoys seeing the animals, both as you walk through the park and on the safari ride. The petting zoo is always a big hit, as is the Festival of the Lion King show.
The other two theme parks offer a great deal for both kids, probably more for the six year old than the two year old. If you have time to do more than two parks, I would probably choose to do EPCOT, then if there is another day, Disney's Hollywood Studios.
Have a great time planning!