Coogie's has the BEST Belgium waffle with bananas and nuts in the greater Los Angeles area! Let me know if you find a better one.
Peach's has the best Belgium waffle with bananas and nuts on top. The service isn't great, but the food makes it worth the trip.
Pop's has great fried food (get the shrimp) and a laid back atmosphere on the water. Come by boat or car.
The Crow's Nest is a neat little restaurant on the water. It has a great view of Snake Island and of the North and South jettys. The downstairs of the restaurant is a casual pub with a great burger and the upstairs is an elegant dining room with one of the best filets in town. Can't go wrong.