The best dive site is the archipelago of Fernando de Noronha. It's the most untouched spot, and it's simply gorgeous on the surface, appealing to everyone. The difficulty ranges from beginner to advance. Best time of the year is from July to December for beginners, all year round for advanced divers. It's one of the most expensive dive sites to go.
The second best is Abrolhos. It's an archipelago some four to six hours from land, where you can't go on shore, so either you make one-day trips or take a live-aboard on one of several boats. The dives are very, very calm, shallow and relaxed, and though the visibility is not as good as Noronha, but the richness of the corals and marine life is incredible. It's good for all levels of experience. Best time of the year is November to March, when it is also possible to watch whales.
The region between Recife/Olinda in the north and Maceio in the south is named the Golden Coast, and here are several excellent spots of scuba diving and the access is much easier than mentioned archipelagos. Around Recife & Olinda is considered excellent for advanced divers, rich of marine life like turtles and sharks, and many sunk ships, but the sea is usually very, very rough. To the south there are many dive friendly spots for snorkeling, scuba dive beginners and also advanced diving. In Porto de Galinhas for instance, is a very pleasant village with many nice sites for good diving and an excellent area for diving courses. In this region the diving is good during the whole year.
The best spots for scuba diving in the south of Brazil are between São Paulo & Rio de Janeiro. Of course they are not as good as mentioned sites in the northeast, but comparing world wide, this region is very good as well. To indicate some spots in the area should be Barra do Una, Ubatuba, Paraty, Ilha Grande and Arraial do Cabo.
Last but not least, there are two islands near Santos / São Vicente where you can take a day trip for two dives - Laje de Santos and Queimada Grande. But it might be very tricky to reach the area: the boat trip usually takes 2 hours or maybe more, and is often rough. Many times the trips are cancelled due to bad weather, so it's always a lottery. From May to July, manta rays are common in Laje de Santos; possible to see ones with a "wingspan" of about 2 meters, and even some big ones, as they can grow up to 6m!
Taking about Diving & Brazil, we shouldn’t forget the country-side town of Bonito, which is more than 1.000km from the sea. This is a paradise of sweet water snorkeling & diving, with beautiful nature and rivers of crystal-clear warm waters with lots of fish. In the region there are also several unexplored caves, where you can practice scuba diving in caves – NOTE: a special certificate is needed for scuba diving in these caves.