Since the meal you'll be having is lunch, I would suggest Sci-Fi over 50s Prime Time, although both are really fun restaurants. First, I think the menu at Sci-Fi (Burgers, hot dogs, milkshakes) is more suited to a lunch and the Prime Time is more suited to a dinner (pot roast, roast chicken, Mom's home cookin').
Also, I think young kids are more likely to be entertained by the cartoons and 1950's sci-fi movie previews than by the Aunt/Uncle/Cousin routine at Prime Time (although that is a lot of fun if you enter into it with the right spirit!)
And Sci-Fi is a darkened restaurant, so the glow-in-the-dark ice cubes show up better in the glass!