If you visit SF and you don't go to Fisherman's Wharf people will look at you funny. It's a tourist trap and for the most part a rip off but I'm not going to blame you for going. It's worth at the very least a quick trip to see it for your self.
For the most part Fisherman's Wharf is a mix of expensive restaurants and some tourist shops selling things that you don't need with the Golden Gate Bridge on it. During the holidays it's jam packed full of people all doing the tourist thing so you won't be alone.
During my last trip to SF I was in the area and in a "tourist" mood so I thought I'd go check it out. It had been some time since I had headed to that part of town for a bread bowl of clam chowder. My advice to you would be to save your money. I was embarrassed at the quality of the chowder that I was served. You're much better off eating away from that area and you'll save yourself some money too.
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At Least Do This: If you do want to eat while you're there the fried shrimp and the crab sandwiches are a fairly good deal. You can find them at the various outdoor stands just outside of the restaurants.
For a good deal on lunch you can head over to Boudin Bakery. You'll see it right in the middle of the wharf area as well as Pier 39. Here you'll find good quality SF sourdough sandwiches at a reasonable price. They have clam chowder bread bowls too.
If money is no object treat yourself to a seafood meal at one of the many restaurants lining the wharf. Keep in mind that you're paying a premium for location. For a better meal check out Crustacean on California Street.
Alternative: There's not much of an alternative here. but my suggestion is to do it early or in the off season. If not, expect lots of crowds.