Well, Fred and Warren's intelligence is shown in different areas than Giles and Wesleys, and in the end these are the one that the competition is between. Buffy has good instincts. Willow is bright. Angelus is cunning. None of them are geniuses.
Between Fred and Warren I'd say the award goes to Fred. Warren and Fred are both fond of making superscience '40s pulp comic style gadgets, but Warren seemed to only excel at the practical. He seemed more of an inventor. Fred was a scientist and seemed to be as good with theory as with the application of her knowledge. Fred just seemed more able to 'think outside the box'.
Between Giles and Wes, I think Wes has the upper hand. Giles seems to be the more effective Watcher and seems to possess a broader range of skills, but Wes appears more knowledgeable. While Giles is referencing his books at all times, Wes seems to just know the answer more often then not.
So, it ends up between Fred and Wes. If I have to choose I'll go with Wes. The guy has a broad range of occult knowledge and seems familiar with just about every language ever spoken (by humans or otherwise). Also, when training as a Watcher they made him 'head boy' *chuckle*. It may not sound like an honor, but when a class full of eggheads say you're in fact the egghead-iest of them you'd have to be incredibly bright.