I think either one would be fun. However, I don't care much for the food at Sci-Fi -- it's just so-so. The portions are big, but the quality seems to waver a lot. The atmosphere is fun, but for a family of four keep in mind you'll be sitting in a "car" -- 2 to a seat and facing forward. Makes conversation kinda hard.
Prime Time is loads of fun, and you can always tell your server that the young ones are a little shy. They can tone down the interaction at your table. I think everyone would have a great time there. The food is also very, very good.