There are two ferry stations in Alameda that go to San Francisco every day; one near Alameda Point, and one on Bay Farm Island. Their individual sites can both be accessed from the East Bay Ferry homepage.
East Bay Ferry
The East Bay Ferry regularly runs between the northern part of the main Alameda island, Jack London Square, Pier 41, and the Ferry Building in San Francisco. It also makes seasonal runs to Angel Island and the AT&T Park. Free parking is provided at the Alameda ferry station. The schedule for this ferry is listed on their website.
Alameda Harbor Bay Ferry
This ferry is next to the Shoreline Park on Bay Farm Island. The ferry schedule is listed on their website. Note that this ferry does not run on weekends, so this should be considered more of a commuter ferry.
Comparisons between the two ferries
Their locations are at opposite ends of Alameda, so it's probably better to aim for the one closer to you!
Unlike the East Bay Ferry, the Harbor Bay Ferry only runs to the Ferry Building in San Francisco, and it does not run on the weekends. Because it doesn't have to make any intermediate stops, the travel times are a consistent 25 minutes, rather than the 20 - 45 minutes it might take the other ferry.
Another important thing to note is that each ferry only stops by Alameda once an hour. However, the two ferries don't stop in Alameda at the same time, so if you're running late it might be smarter to travel the extra distance to the other ferry.