We have done Stingray city several times. We recommend Captain Marvin's. His company started the whole thing. He offers newer boats, few people, and options such as a two reef snorkel trip prior to the stingrays, a conch luncheon prepared on a beach and friendly crews. You get off the tender, turn left they are in a little store front on the other side of the street. If weather is bad, and you have to cancel, there is no charge.
Tranfers to and from his boats. leaves you off right across the street from the pier so you can head back or window shop.