Please come to Naples and visit the Naples Botanical Garden if you have time! I work there. It depends on how long your trip is of course.
I second RF Orchids in Homestead. A treat.
Vizcaya is nice, and of course Fairchild Tropical Garden in Coral Gables. That can take you a day to get through.
The Fruit and Spice Park is great when they have a festival, otherwise really just if you're into tropical fruit.
I agree to book something ahead, and Marathon is the 'middle key' and therefore pretty central and not as pricey as Key West.