I just took my son to the Children's Museum in St Paul tonight for the first time (they had a special birthday celebration that I got an invitation to), and it was GREAT! I am going to get a membership ($80/family/year) and try to go at least once a month. My son just LOVED it! There is so much to do... but we only saw a tiny part of it. He was having soo much fun in the first areas we got to... restaurant and grocery store, that we didn't get any farther than that. It was set up for them to just explore and pretend, cash registers, a whole kitchen, shopping carts, even mail and everything. He would still be playing if he could. He can get so much out of the experiences he has there, and loves every second of it.
We also have a yearly membership at the MN Zoo- $55 for individual plus 1 guest, children under 3 are free, and parking is free. My son was 16 months when I first got a membership there, and is now 3. We have used it more than enough to be worth it, and he loves it there. It is great in the summer when you want to get outside, you can get exercise, they learn, and you all enjoy being there. It is also great in the winter, when I was a nanny we would go there every week, and walk through the tropics trail. We went right when they opened at 9 am, just left the house after breakfast. We got done at naptime, and both kids were completely out in the car. It kept us busy.... if I don't go somewhere the day just passes by and I feel like it was wasted. That was something the kids loved to do. There is so much to see, that they get something new out of it every time. Even now. Members also get half off the monorail, so for $1.75, you and your son can ride the train and see everything from above. My son loves that too... he gets to ride a train... and get a different view of the animals.
I am guessing in Eagan you have been to the wooden park on Cliff Rd? I'm not sure of the name, but it looks like castles. It is great! If you haven't been there, you should try it. I also bring sand toys there, there's lots of open space to play in the sand and build. That's my favorite park. But you said you live in Eagan and go to neighboring parks, so I am sure that is one of them. It is between 35W and 13.