The weather here can be anything between the 60s and 2 feet of snow this time of year. So be prepared with both indoor and outdoor options.
Outdoors, we have a very nice Zoo, which is just down the road from the Science Museum if the weather is bad.
I also like to take my son to the Botanic Gardens, which is near the Zoo. If the weather is nice, the fountains are on, and there are lots of paths for the kids to run on. You have to make sure they stay out of stuff as it's not designed for children, but it's great for crawlers and early walkers -- a park with absolutely no dog poop or cigarette butts. And they have an indoor tropical area with a giant "tree" that my son loves.
The Butterfly Pavilion is also a fun tropical place to go in the winter. They have lots of interactive exhibits that are great for older kids.
I agree with Whizzy, the Art Museum here is very kid-friendly. I was pleasantly surprised when I took my 2 1/2-year-old at how child-oriented they were.
If your kids are a bit older, the Pearl Street Mall in Boulder is fun, and a trip to the Dushanbe Tea House. You can also do some nice, little hikes around the Chatauqua.
The Aquarium is, to my mind, a bit over-priced for the smallish size, but is just right for a toddler-sized outing. And the Children's Museum is next to the Aquarium and right down the street from the REI.