Here at home (San Francisco) I vote for Farallon.
I heard so much about Aqua, but my experience there was far from memorable: food came cold, service was rushed.

Overseas, I love a place in Cascais, Portugal called Porto Santa Maria. Normally, service and/or food aren't good in restaurants with a view, but this is an exception.
http://www.portosantamaria.com/uk/kitchen/ecozinha.htm