For a day on San Francisco Bay you should bring a bathing suit and a parka, and you'll probably use both. Seriously, you should bring warm clothes and a wool cap as well as shorts and a t-shirt. Deck shoes are advised, meaning flat-bottomed, rubber-soles shoes, but not black-soled, which tend to scuff up the deck. We have sunny days--shorts weather--in the middle of winter, and in summer our notorious wog, wind with fog. The most reliably good weather is in spring and fall.
Seasickness usually isn't a problem within the Bay, and we don't advise guests to take seasick medication unless they know they are particularly susceptible. The only part of the Bay that has any significant wave action is in the slot, from under the Golden Gate Bridge east to Alcatraz. This is a narrow band, and smooth water is never far away.