Rare honesty in a comparison page: Brian Epstein guides out of Key Largo and co-owns a fleet in Islamorada. He wins either way, so you get the real answer.
Key Largo is the backcountry and convenience pick. It is the first Keys town, about an hour from Miami, and its side of Florida Bay is a maze of flats, creeks, and channels built for light tackle: tarpon, bonefish, snook, snapper, and the night trips almost nobody else runs. One captain, one bay boat, your hours.
Islamorada is the offshore pick. Twenty minutes further down US-1 gets you the sportfishing capital of the world: the famous reef edge, the humps, and the family's four-boat fleet, the Poppa Wahoo Collective, including a 55 foot Hatteras running deep sea trips, overnight swordfish, and evening sharks with rates posted.
It is one family. Tell either dock what kind of day you want, backcountry or blue water or both across two days, and you will be routed to the right boat. That is not something the other comparison pages can offer.
Key Largo's protected backcountry, or Islamorada's nearshore bay boat trips. Calm water either way; pick by drive time and your hotel.
Islamorada, by reputation and geography: the humps and the edge are its home water, and the family's Hatteras fleet is built for them.
Easily, and people do: backcountry day out of Key Largo, offshore day out of Islamorada. Same family, two docks, one phone call each.
Captain Key Largo and The Poppa Wahoo Collective are the same family. That means nobody here has a reason to talk you out of the other island. Pick the water that fits the trip.