I've been to both, and 50's Prime Time Cafe definitely has better food.
I liked the atmosphere of the Sci Fi Cafe, but if I remember correctly, I saw the same footage over and over again on the "drive in" screen, and the food was so so (to me comparable to Pinnochio's CS at MK). You'd think they could get at least an hour of footage to loop, rather than around 20 minutes worth, which meant we saw the same footage at least 3 times.
It was kind of a one-time-only place at the Sci Fi Cafe (and I LOVE old sci-fi). I wasn't that impressed by it.
But I went to the 50's Prime Time Cafe twice in the early 1990's and loved it! Yes, it's very crowded, but we had a lot of fun, and the food is better.
If you're going to go to Sci Fi, go for a late afternoon snack (like a milkshake), and you'll stay just long enough to see the "movie" loop only once.