We always make a PS no matter where we are going or what time...BUT, you are going at a very low-volume time and probably won't need.
Hard to choose for a 3-year-old. Honestly, both will probably go over his/her head. Prime Time atmosphere is like a diner....or a kitchen from a 1950's suburban American home, with television shows from that era playing in the background.
Sci-Fi is a 1950's-era drive-in movie theatre. You sit in "cars" and face a large movie screen in the dark that plays little movie clips from that era's science fiction flicks (the really hokey ones like "Attack of the 50 Foot Woman!")
Our kids are 15, 11 and 7 and honestly, they don't understand any of it! Two weeks ago, we went to Sci-Fi and they enjoyed it, primarily because of the cool atmosphere of sitting in the cars and having a nice juicy cheeseburger, fries and shake.
Your 3-year-old really won't understand either place......and the darkness of Sci-Fi, along with the "scary monsters" on the screen may scare him/her...so keep that in mind. If you think your child may handle that, though, and you and your spouse are into either of those things, then give it a shot. We always found both restaurants a treat more for my wife and I as opposed to the kids.