If you are comfortable being near a marina, then yes, the Marina district would be ideal. While it isn't in San Francisco, the town of Sausalito is very close by in Marin county and there is a whole neighborhood of houseboats (er, floating homes) located there.
Better Homes & Gardens/Mason-McDuffie Real Estate
2200 Union Street
San Francisco, CA 94123
As Toby indicated, it is very difficult to find housing right on the water or right on a marina in the Marina District of San Francisco. I would most definitely recommend seeking housing in South Beach or Mission Bay. There are existing buildings there and new developments like The Madrone which will be offering a total of 329 new homes in Mission Bay. As of today (4-18-2012), the Madrone has 125 homes in contract and they are moving fast. Here is a blog I wrote about it at the end of December: http://www.sfnewdevelopments.com/9336/the-madrone/
Here are links to areas that I think may suit your needs:
Best of luck to you in your search!