We absolutely love The Cape and go every fall (for the past 10 years).
Check out kidsonthecape.com for some ideas.
The beach will keep the kids occupied for hours, the National Sea Shore in Eastham has very large waves, a beautiful beach, but not great for the little ones. Note: expect to pay $10 to $20 for parking at most of the beaches.
If bike riding is your thing, be sure to bring the bikes along as there are tons of great trails all throughout the cape.
In Sandwich (when you first get onto the cape), can't remember the name, but theres a small museum type place, very kid friendly, that tells about the building of the canal and has some hands on exhibits. It's about a 1/2 hour stop.
There's a nice trail that runs along the side of the canal. We usually stop there to take a nice walk and stretch our legs.
If you take a drive into Hyannis, visit the Kennedy Memorial. Next to the memorial is a nice little park, with a picnic area, playground, and small beach. If you continue on down the road, there's a larger beach that's also nice.
In Yarmouth is the Zooaquarium. We went there years ago and were very disappointed. Of course, things could have changed so you may want to check out recent reviews.
As for eating, we're really big on picnics, so the cooler is always with us. We all love The Brazilian Grill in Hyansis, but it doesn't cater to younger kids. Ok, not healthy but we're on vacation, we love to pick up KFC and take it down to the beach. There's also the Hearth and Kettle, which is very family friendly and has several locations. For fried seafood (the have hot dogs for the kids) the Kream and Cone on Route 28 (I think it's in Dennis) is great.
Have a great vacation!