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 operators of the Peter Pan bakery make the best donuts I've ever tasted. This place is charming to its core. Decor and presentation: circa 1971 & virtually unchanged since.
For brunch, the classic dish to get is the Feijoada, but the benny is also solid (and i don't recommend a benny lightly)—you can also ask for ham and spinach together (my favorite). For dinner you can also get the same thing, or the Moqueca (shrimp stew) is incredible. Pro-tip: if you're there for breakfast on a weekday, ask for a egg and cheese (add bacon or ham or avocado) on a croissant. Not on the menu—sounds basic, tastes amazing.