If you’re inclined to go snorkelling, travel agency Ile Mandiri Tours and Travel can help you out, providing transportation and equipment rental. Beliko beach has a stand of coral reefs that can be quickly reached by an outrigger boat, and is about an hour from Larantuka proper. Watch out for currents here, and book in advance as the tides are not always amiable to snorkelling.
There currently is no scuba diving operator in Larantuka, although the area may have some potential. Ile Mandiri travel agency owner Chris Hansen is a professional salvage diver, and is working on getting his centre PADI certified. Ask him if you’re deadset on getting a dive in here -- only advanced divers need apply at this time, as the currents can be a real bear and there’s little infrastructure to support divers.