Both restaurants have an interesting atmosphere. Sci-Fi Drive-In should be a hit with children that age; they get to "eat in cars" and watch promos for old low-budget sci-fi flicks, with a few cartoons mixed in. 50's Prime-Time appeals more to adults, especially those old enough to have been children during that time. But the servers there are playful and help to entertain children.
The food is good at 50's, large servings of "comfort food" such as pot roast, meat loaf, and fried chicken, and not too unreasonably priced for Disney.
The food is fine at Sci-Fi if you stick to burgers and similar food; we've only had lunch there, not dinner. It seems to be more expensive than 50's Prime Time.
I would recommend doing the opposite -- lunch at Sci-Fi; dinner at 50's. But I'm sure you'll enjoy it either way.