This comes too late for the OP, but my favorite waterfront dining option is Guaymas in Tiburon (http://www.guaymasrestaurant.com). It's an upscale Mexican restaurant literally right at the ferry terminal in Tiburon. The food is very good (but not amazing - I just have to give that caveat given that the Bay Area DOES have lots of food that IS amazing), but the combo of the food and the setting is perfect. The main joy of dining there is to take the ferry from SF to Tiburon. You get off the ferry, go for a walk if you want, or step right over to the restaurant for lunch or an early dinner and drinks. And when you're done, you hop back on the ferry for an amazingly beautiful ride.

I now live in Denver, but when I lived in the Bay Area my partner and I used to take our bikes on the ferry, then do a short ride in Tiburon, followed by lunch and then the return ride. Always a wonderfully relaxing way to spend a weekend afternoon. Just be sure you check the ferry schedules in advance!!

And for an even more complete itinerary, do this on a Saturday and arrive first at the Ferry Building in the morning for the farmer's market. Grab breakfast there, do some walking or biking, then head up to the Tiburon ferry and off you go.