Depends. Are you going to rent a car, or is somebody going to pick you up, or what?
Fort Lauderdale is only about a half-hour longer drive from the Keys, the airport is less congested than Miami and easier in and out by car, and usually rates are lower to Fort Lauderdale than to Miami.
But if somebody is going to pick you up when you arrive and drop you off when you leave, sometimes Miami is more convenient.
There are shuttle and limousine services available from both airports to the Keys, and Greyhound has a regular schedule from Miami Airport to the Keys (by far the cheapest, at about $15 one way), if you can connect timewise.