Florida is a huge state with varied geography, culture and economics. Each area has wonderful marinas, but it really depends on what you are looking for. If you could be more specific, you might get better responses. North/south, fresh or salt, proximity to an inlet, live aboard or not, full service Marina, amenities such as pool/tennis/golf, budget concerns, etc.?
If the boat is there year round, you also have to consider hurricane protection to your insurer's satisfaction. This can dictate where you pick too.
We are in Palm Beach and love it. Friends are in Ft Lauderdsle and live it. Other friends wouldn't be anywhere than Jacksonville. Still others swear by The keys.