The Dolphin Explorer is run by the 10,000 Islands Dolphin Project, and their unique approach makes it the best dolphin tour on Marco Island.  Rather than a regular tourism endeavor, it is first and foremost a scientific one that's been going on for a couple decades.
The team "tracks and monitors the social behavior, movement, geneaology, and habits of the bottlenose dolphin population in the waters surrounding Marco Island."  The tracking is done by photo identification rather using a tracking device---the dolphins' dorsal fins act as their fingerprints!  (Absolutely wild.)
The research is fully funded by the tours, so they don't have to rely on the fluctuations of grants or donations, which means they've been able to do this continuously for almost 20 years and have an amazing amount of consistent data on generations of dolphins.  It's the only one in the United States that engages with and is supported by the general public.
They even occasionally help in dolphin rescues!