I also love San Angel Inn. As far as atmosphere is concerned, it hands down wins. When I went to the Coral Reef Cafe I found it's food to be good, but nothing special. It's nothing you couldn't get at a nice seafood restaurant at home. The aquarium is nice, but what could be a beautiful view is generally slathered with kids pressing their nose up against the tank to see the fish, not that there is anything wrong with that, but if you are looking for a focused pleasant experience as an adult you may not get it. Also the room for the Coral Reef Cafe is a big box with a glass wall: the noise is pretty awful at times. It doesn't have anything to do with the crowd being particularly rowdy, it just a bad room for acoustics so it sounds like a school cafeteria.
I would go for San Angel Inn. The last time I visited the food was wonderful and you can' beat sitting by "El rio del tiempo". Sure it's a little noisy there as well, but it fits with the market place/town square theme.