I haven't fished there in decades, but if you are thinking about boating in the shallows of the upper bay, be careful. Water conditions can change from calm to rough very carefully. Most of my shark/ray fishing was along the Eureka channel. Mud (brown smoothhound) and leopard sharks and bat rays are fairly common there, with the best fishing after dark.
The last time I fished there, we fished off cannery docks. Those are all long gone.