My son has never had a problem with the atmosphere at the Rainforest Cafe but he has been going to WDW since he turned one so he is pretty used to loud, fast and "jump out at you" things.
There are several rooms at the Rainforest Cafe. I remember the gorilla and elephant rooms. It seems like there is a room called something like the fish room?
If the restaurant is not super crowded and you don't mind waiting, you can request a table that's not right beside the gorillas or the elephants.
The thunder isn't super loud. The lights will flicker and then go dim. After that, you will hear all the chants of the gorillas and the trumpeting of the elephants.
My suggestion would be that you arrive a little early, take your children on a tour through the Rainforest Cafe store (you can see into the restaurant) and let them get used to the noises of the restaurant.
Hope you have a great trip, Lisa