I live near Medellin, and I really love it, but it's more a lifestyle place than something with a lot of tourist attractions. The advice from JohnnyColombia is spot on. You definitely want to book some day trips out of the city, as the countryside around the city is beautiful and mountainous. Note - Guatapé and El Peñól is a good choice, and we always take visitors there, but do spell it as Peñól, not Peñón.
I also recommend the Medellin zoo.
One place you might enjoy with your kids is Tutucán, which is an amusement/ecological/water park in Rionegro. Here is the website:
http://www.comfama.com/contenidos/se...-familiar.html
We have kids in the same age range, and they love going there. It's not anything huge and fancy like a 6 Flags, but there is plenty to do for a day.
You might want to consider a few days in Medellin and a couple of days in the Rionegro/Llanogrande area. You have to pass through Rionegro on your way to Guatape anyway.