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Pier 49 is the big touristy pier area with a Bubba Gump and the popular clam chowder in sourdough bowl place, etc... but I actually like the east side piers (on a map, Pier 27 and southward toward the ferry building (which houses a day market -- maybe not useful to you) there are some neat warehouse based taverns and stuff there.
I like the Mission district myself for restaurants and stuff. If you like baseball there's Oracle Park there for a game if the Giants are in town perhaps... it's a cool location on the waterfront... the BART is around for cheap traspo but it can be a bit sketch at night lol
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