I mean, they're really not related at all, aside from both being based on somewhat questionable movies.
Shadow is mode based, Congo isn't. Shadow has an upper playfield, Congo a lower. Congo is more traditional, normal plunger, pops, Shadow has neither. Congo is a relatively easy game, Shadow is pretty hard.
You really would have to play both and see what you think. I wouldn't mind owning a Congo sometime, but I've seen them for prices I could afford and passed them up. Shadow is probably the most keeper game I have. To me Shadow is far superior, but Congo is still a cool game.
Shadow is more challenging, has more intense original gameplay, has better sound, just overall a better game to me.