Having the experience of owning and running a coral reef aquarium (and frequenting this particular shop about once a week) - I was sad to hear it closed it's doors. Their reef display tank was always amazing. These pictures were taken from PetCo at Union Square (I also used to go there for my saltwater needs).
The best underground shows you will find will have free pbr and models as far as the eye can see. They are rarely announced, so keep your eyes out for promising openings, especially with Milk Underground coming up.
This quaint shop boasts an artfully arranged and tastefully curated selection of jewelry, pottery, books and art. I have to keep myself from going there too often, because I have trouble leaving without making a purchase.