East view:
Epic Roasthouse
Waterbar
Slanted Door
Waterfront Restaurant
Butterfly

West View (for sunsets)
Cliff House
Beach Chalet


However great the scenery might be, the waterfront dining options are pricey and nowhere near the culinary accomplishments of other "inland" restaurants.

Here's a thought: if you want good waterfront experience in San Francisco, try out The Ramp for lunch, if it is sunny when you're in town.