I had spring conferences for 4 years straight in the same manner, I booked extra days and hopped along the keys in search of bonefish. Finicky fish but my best was an 8# at Bahia Honda - a MUST to visit.
First on the list is Pennecamp State Park, Key Largo. Easy access but watch the tides and second the footwear advice. You can also step on critters like rays down there and need protection on the tops of your feet as well as bottom and sides. If you have limited time just blow right past this area, there's much better stuff ahead.
Then the usual stops at shops in Marathon, Islamorada, etc - you have to poke around to find good shore access to flats. There was this one place I stayed in Islamorada, it was some guys house. Everyone there was a bonefisher, and you could walk the shore for bones. I can't remember what it was called but it's a great little insider's secret. Across from a major campround, house painted a yellow/khaki color with decks on the water and the office was his kitchen. It was $75 / night but when you factor the DIY fishing into it well worth it.
If you are goin' on your own I'd spend a day at least on Bahia Honda State Park. The latter allows camping but are booked way in advance. Kayak rentals available, just one of the most gorgeous places on earth.
Two spots I got fish on my own - the Green Turtle Inn sign at Matecumbe, a public stretch of land and Bahia Honda lower keys. Good spots to fish on your own.
Ben Iannotta who wrote the Miramichi article in Chronicles guides full-time on Summerland Key, PM me for contact info.