p.s. Fisherman's Wharf is their equivelent to Navy Pier (I would only go there for amusement and to see the cool seals sunbathing on the docks)
NOW I WANT TO GO !!!!! bah-h-h-h-h--h
Point Reyes National Sea Shore is (15-20 miles?) each way out to the lighthouse and you can ride to or back through Marin and across the Golden Gate Bridge. The peninsula gets narrower and narrower until you start to see ocean on both sides. http://www.nps.gov/pore/ It is ~25 miles from SF so it's a pretty long, hilly, one-day trip, but if you can rent or transport a bike out there, it's not to be missed.
If you've never been to Muir Woods (and maybe even if you have) , ride to and from across the Bridge.