Choosing where to go for the day is the easy part, and other pages handle it. This one deals with the part that decides whether the day works: when you leave, when you are back, and what condition the evening is in when you get there.
Leaving Miami costs more time than the map suggests in one direction and less in the other. West on US-41 to the airboat belt is 30 to 45 minutes from Brickell with almost no traffic to speak of, which is why a half-day trip out there is genuinely a half day. South on US-1 towards Homestead is about an hour going out and can be considerably worse coming back on a Sunday afternoon, when everybody who went to the Keys is returning up the same two-lane stretch at the same time. North to Fort Lauderdale is the one leg where the train beats the car, at roughly half an hour from the downtown station, with no traffic and no parking to solve at the far end.
The return clock is the number to plan around, because it decides what happens to the rest of your day. A trip that puts you back at two leaves you an afternoon, a shower and a proper evening. A trip that puts you back at six puts you in the worst causeway hour of the day, which matters enormously if you are sleeping on the island and not at all if you are not. A trip that puts you back at eight has taken the evening as well as the day, and on a three-night visit that is a meaningful fraction of the trip.
Then there is the question of whether to drive yourself or buy seats, which is almost entirely arithmetic rather than preference. For one or two people, a booked trip with pickup is usually cheaper than a hire car once parking, fuel, tolls and the rental company's toll administration charge are counted. For four or more, the car wins on money and wins again on flexibility, because you choose when to leave and you are not waiting on a van collecting three other hotels. The crossover sits at about three people, and it moves in favour of the car the further you are going.
One warning before the tables. A day trip is not a slot in a day, it is the day. The most common planning failure on this site's postbag is somebody stacking a half-day Everglades trip in the morning, a beach afternoon on the far side of the bay, and a dinner reservation somewhere that needed a causeway crossing at seven. Pick the trip, then plan a quiet evening within walking distance of where you sleep, and you will enjoy both.