MMM is definitely not the best place to look for fancy seafood restaurants on the water, but I'll bite anyway :)
The first thing that came to mind is
C-Level. On the water, close to downtown, good food and nice ambience for a special occasion. It's the less expensive version of Island Prime, which is adjacent. But it is still not cheap, because, you know, it's San Diego, seafood, and on the water. I thought of it because I actually took a Celiac there and they were very accommodating. They went in detail through the menu for her and even fried her chips in separate oil. Tip: their whole lot is valet so park on the street somewhere along harbor island. This way you also get a beautiful walk along the water with a city view on the way there and back!
If you're not looking for ambience but just great seafood, this is my favorite place:
https://www.yelp.com/biz/blue-water-seafood-market-and-grill-san-diego?osq=seafoodThis is very casual and on the water/outside:
https://www.yelp.com/biz/point-loma-seafoods-san-diegoHope you enjoy your trip to San Diego!