Where to buy fresh seafood and fish in San Diego
I would recommend the following to you:
Catalina Off Shore Products, you need to know what you want when you go there, they are not a market, but a wholesaler that also sells to the public and they have great prices.
They prefer cash, but will take check or credit it the order is over 25. http://www.catalinaop.com/
Point loma Sea Food in Point Loma. they have a great selection.
If you're looking to make blue crab cakes like they serve in Maryland then I've noticed several of the local Asian markets are now selling live Asian grown blue crabs. Lucky Seafood and Seafood City in Mira Mesa (among other places) now has them in stock and since they're live you know you won't be able to get anything fresher. The downside is you'll have to steam and pick the crabs yourself which can be a pain but if you want that authentic Chesapeake crab cake taste there is no better way to get it without flying to the east coast.