Boma is much better food. Also, there are so many Rainforests throughout the country, that I'd rather go to a place only in WDW.
My kids liked Boma. I'm not sure what your kids are like, but my middle son does not like Rainforest because of all the "stuff" going on there. He's eaten there twice (in Chicago) and really is not happy there.
Boma has lots of kid friendly choices, more exotic food for adults (if you want that but also some basic stuff) and phenomenal desserts. Plus, you can see AKL which is a beautiful resort.