Tons of great ideas in here so far! Whatever you manage to fit in, it will be a great trip. My kids are about the same age (8&11) so I'll try to throw in some ideas for stuff that they like too.
Boulder
I agree that the Celestial Seasonings tour is fun (and free!) and totally worth it for the mint room alone.
The Fiske Planetarium is also really neat if your kids like space, and there's often a Groupon deal for it.
Motomaki is one of my favorite places to eat up there. Sushi burritos are great!
Estes Park
I agree that the Fall River Road is a great drive through RMNP. Is your 10-year-old in 4th grade? If so, you can get a free national parks pass:
https://everykidinapark.gov/ The Junior Ranger program is cool too. The Alluvial Fan is a fun place to climb around the rocks and play in the water.
Definitely take the Peak-to-Peak scenic highway on the way there. You can also make it a loop and go out the west side of the park and down through Grand Lake and Winter Park to get back to I-70. This adds some drive time but you get to see some more scenery. And you can stop in Idaho Springs at the original BeauJo's location for some Colorado style pizza. We love their food and that location is in a cool old building.
Denver
The Denver Zoo is fine but personally I don't find it to be that unique or special. I'd probably pick the Cheyenne Mountain Zoo over it just because the setting is so different.
The Denver Children's Museum is a great place to wear the kids out. They have a cool new outdoor area opening soon that looks awesome.
The REI flagship store is just down the road from there and worth a visit. It also overlooks Confluence Park where the Platte River and Cherry Creek come together. You'll see a lot of people playing in the water there and riding inner tubes. And right next to it is My Brother's Bar which has some of the best burgers in town. Then walk up the hill to Little Man Ice Cream.
Definitely check out Red Rocks. Walk around and see the museum.
Edit: if your kids like dinosaurs there are several good spots near Red Rocks to see: the Morrison Natural History Museum and Dinosaur Ridge. Lots of fossils in that area!
Colorado Springs
My kids like the Cheyenne Mountain Zoo a lot.
Garden of the Gods is great and there are some places where the kids can climb on some rocks and have fun.
We like Manitou Springs a lot too. Cave of the Winds is neat if you like cave tours (I really like caves). Keep an eye out for Man-Bear-Pig! There are some cool cliff dwellings nearby too (they're a recreation, not authentic, but the nice part about that is that you can climb all around in them unlike Mesa Verde):
https://www.cliffdwellingsmuseum.com/
Pikes Peak is a great view and worth the drive up.
Have fun!