I too have to say Universal. Although I love Disney Studios, I just think that Universals theme is so much better. MIB, Shrek, Jimmy Neutron, Simpsons, ET just to name a few would be a treat for your kids.
I have to disagree with one poster who stated that the lines in Universal were worse than Disney. In the 9 times that I have been down there, the lines in Disney have been WAY worse than Universal. If you get to Universal early enough, you can get through the best part before lunch without really every waiting in line. I have never experienced this in Disney - EVER. The first hour of the morning may be ok, but it was a tactical job for all involved - i.e.: "Honey....I'll meet you at ToT while you go to RnR coaster and get fast passes for us so we won't have to wait as long in line". I have never had to do this EVER at Universal.
But, I guess it would be dependent on what your kids like. If your kids like super heroes, Dr. Suess or Harry Potter, than maybe the Islands of Adventure side at Universal would be their thing. If they are more like the rides I mentioned at the beginning, then maybe the Universal side is for them. But, if they are into Star Wars and princesses, then maybe stick with Disney. I will say this....my 14 year old step son will never go back to Disney. He LOVES Universal WAY too much now that he can go on all the rides!