Pier 39 is an absolute must stop on your way around San Francisco. It is true that the locals will often avoid the area as it can be a little too touristy, but don't let that stop you because it is a fun place to come for lunch.
Pier 39 and its neighbor Pier 41 are on the edge of the Fishermans Wharf part of San Francisco which is known for its large promenades, cafes and restaurants.
The pier stretches into San Francisco Bay and is full of different places to stop for a drink or food as well as some quirky shops. You'll get great views of Alcatraz Island right ahead as well.
The real reason you have to come to Pier 39, however, are the seals that have decided to make the wooden platforms and parts of the pier their home. There anywhere from 150 to well over 1,000 seals at Pier 39 depending on the time of year and nobody seems to be entirely sure why they picked this particular spot.
To get more insight into the seals and other local sea life, make sure to drop into the Aquarium of the Bay at the foot of the pier. You'll see everything from jellyfish to large sharks and there's a whole section dedicated to the seals.