In battle, Unown is definitely better.
I don't understand why you would use either, but if I had to have one or the other, Unown would be my choice, simply because of its better offensive power.
If you look at Magikarp's stats and movepool, it learns only physical moves. The problem is that it has a base Attack stat is only 10, giving it horrible attacking power.
Unown, on the other hand, is not only cooler out of battle, but is better at battling. It has base Attack and Special Attack stats of 72 each, and despite the fact that having only one move makes it pretty predictable, the fact that Hidden Power can be any type really helps it out.
So to answer your question, don't use either in battle, but if you had to pick one or the other, choose Unown, due to its better power and the fact that its move type is unpredictable.