I lived there for 4 years and I honestly cannot say what you would do with a 1 and 3.5 year old for a holiday there.
There are various zoos, wildlife parks, water parks etc, but nothing exciting, well probably for a young kid it would be.
Be prepared to be ripped off by the taxi mafia in Phuket and Samui.
There will be some sort of elephant trekking nonsense that you can go on, probably a croc farm as well.
If you were on your own or with a partner I would be telling you to get off the beaten path and look around real rural Thailand to see what life is really like.
When I first went there when I was traveling the world, I used to get local buses to wherever I fancied and just see where they took me, slept in some strange places, and met some really odd people, but it was all good fun.