Bonefish Bob's in Islamorada is a must! He was my bonefish mentor... the over-the-counter advice I got from him years ago led me to my first DIY success and thus my current crazed state over flats fishing.
Worldwide sportsman in Islamorada is a good spot, lots of history there.
Check out Bud and Mary's Marina for advice, boat rental, guides, etc.
Down at Key West stop in at Saltwater Angler, which used to be Jeffery Cardenas' shop. It looks like it's tied in with the Hilton now.
There are other shops along the way on the main drag, hard to miss. The ones I saw last time there are probably gone and new ones sprung up but the above three are still there.