We took two three year olds - a boy and a girl. Fantastic! We were worried we were going to run out of things to do, but it was more that we had more to do than we had time for. We saw a film in the Imax, specifically for youngsters, and it was perfectly pitched. There were lots of 'hands on' activities for the children to do, and the science garden is really well considered. My 3 year old was enjoying it so much she put her all in one on and carried on playing in the rain so she could work out how to do the lock system on the miniature canal.
You can get a reduced price for entrance if you travel there on the train - it is a short walk from Moor St. You can take your own food, but the cafes by the entrance are reasonably priced and I was pleased with the range and quality of food available (I am very funny about what my daughter eats).
My only (pretty large) disappointment was the train. I have very fond memories of seeing it move when I was a youngster, and it does not move anymore ;C
We will go again - lots.