Both of the restaurants you mentioned
are a lot of fun! One thing that might help sway you one way or the other is that the set-up of the Sci-Fi Dine-In Theater doesn't really encourage family conversation. You are seated in rows of a car, so you won't all be facing each other. Also, there are movie clips running which serve as a fun distraction and often times leave guests sort of mesmerized with what's happening on the big screen.
The 50's Prime Time Cafe is pretty much the exact opposite. It's interactive fun for the whole family!
It's hard to compare the food between the two because while one serves comfort food favorites, the other is more a burger/sandwiches type of place. I can tell you, though, that I've never had a particularly bad meal at either restaurant.
But--just to complicate your problem--I would also suggest
Mama Melrose. My family absolutely loves the cozy atmosphere and, in my opinion, the food here trumps that at the other two restaurants. The twinkly white Christmas lights add such a whimsical touch it's just fun the moment you sit down!
Good luck with your decision!