The history museum will take longer because there are so many exhibits. Unless you like staring at animals for a long time, but if you are going with kids I doubt each animal will interest them long, so museum is my final answer.
I'd go with the natural history museum, those places are incredible, there are so many different exhibits, and each exhibit has something fascinating. The one in New York was breathtaking. I'm sure the one in Colorado will be a treat as well.