Other than "unique San Diego restaurants" or the "best fish tacos" one of the most frequently asked questions - especially by those moving to San Diego - is where to buy good fresh fish. The usual suspects are Point Loma Seafood or Whole Foods, with occassional recs for The Fishery or the Fish Market. Having grown up in SD when there actually was a tuna industry and a wide variety of fish markets, about where Seaport Village now sits, finding good fresh fish now seems to be something of a challenge, a rather expensive challenge at that.
You may have seen Maria C. Hunt's generally favorable reivew a couple of weeks ago about the restaurant Blue Water Grill. They also sell fresh fish, very fresh fish, very good fish. I haven't eaten in the restaurant portion of this place, but I have purchased quite a bit of fresh fish from them.
Selection is small, usually 5-10 varieties. They will bone for you, and even better, they weigh the fish AFTER boning, so you don't pay for what's going to be discarded. I've had their Alaskan halibut, red snapper filets, and mahi-mahi. All of it has been exceptionally good, on par with Point Loma Seafood, maybe a tad better than Whole Foods. They also have sea bass, salmon, ahi, ono and some of the other usual suspects. Prices are about the same as PLS and WF. There is also a selection of shellfish.
Also in the "L" shaped fresh fish case, and definitely worth investigating is the house-made ceviche. The last time I was there it was a mixture of yellowtail, mahi-mahi and snapper. It's the fishmonger's grandmother's recipe and the fish varies depending upon what's plentiful and available. It is very flavorful and packs a kick from the chiles. They will give you a sample of the ceviche.
Blue Water Grill is located on India St. about a block South (towards the airport) of El Indio. It's on the Northbound, one-way part of India, that runs paralell to I-5. Mostly street parkign that can be somewhat difficult depending upon day and time of day. Parking is easier than either PLS or the Hillcrest WF.