If you plan on wading, wear something that will protect the bottom as well as the sides of your feet to protect yourself from cuts on coral.
On a flats boat you will have a fair amount of line at your feet so that you can make a quick cast when you see a fish, as a result, I tend to wear boots without laces. You want to minimize wearing anything that your fly line will hang up on. If you have boots with laces, bring some duck tape and tape your laces down.
have a great trip. I assume you will be fishing for bonefish, but there is some good baby tarpon fishing and you might want to bring an extra rod for them.