On my recent South American trip I visited a few more zoos whilst on transit.
Bogota, Colombia - Bioparque La Reserva and Parque Jaime Duque (+Salt Cathedral): A trip which really needs a taxi to be hired for the day and you'll need to have directions available or the driver to have a GPS system as they struggle to find La Reserva. Bogota evening traffic is horrendous, so I almost missed my onward flight. 24h left luggage facilities in the airport are near domestic arrivals.
Santa Cruz, Bolivia - Again, a taxi is probably needed to visit this zoo which is around 35 minutes' drive from the International airport. Left luggage facilities at the airport.
Parque de las Leyendas, Lima - The zoo is conveniently located half way between the airport and the city centre. There is a left luggage facility at the airport (head into domestic arrivals). Once more, taxi is the best way to access the zoo. Typical cost is about 20-30 soles.
Buenos Aires, Argentina - Across the road from Jorge Newberry Airport (Aeroparque) is the Club de Pescadores, which has a small aquarium within. Although it sits on the sea opposite the airport complex, it's about a 20-minute walk from the airport exit. If you choose to take a taxi then do not get it from the airport taxi stand; cross over and go out to the main road (near the bus stops) and hail down a passing taxi - using the meter (fare 1) they'll only charge a minimum fare [roughly 15% of what the waiting drivers would quote].
Curitiba, Brazil: The airport and zoo sit to the south of the city; surprisingly it still takes about 30 minutes to get from one to the other and taxi seems to be the only way. Passeio del Publico, the old zoo, sits in the city centre and so transfer from the airport should be easier. Be aware that neither has an entrance complex or facilities for left luggage. The airport has a service with limited hours (lockers attended from roughly 9-3 on weekdays and Saturdays, but no Sunday service)
Villavicencio, Colombia: The small airport caters for flights mostly from Bogota, with the last departure shortly after 5pm so I don't think it's much of a 'transit airport' but the zoo (Bioparque los Ocarros) is a couple of minutes away in a taxi so it's an easy trip should you find yourself near here.
Visits from which I've gone directly to/from an airport or which seem like practical transit zoos:
Guarulhos Zoo, Brazil - about 20 minutes from Sao Paulo's busiest airport is this small, free zoo which houses a number of interesting animals. Again, a taxi would be required to visit and it's probably best if you ask them to wait for you (depending on price). A visit to the zoo doesn't take too long. Alternatively the cafe outside the zoo is now able to call a taxi for you if you choose to request another for the return trip. There is nowhere to leave your luggage at the zoo.
Iquitos, Peru - both CREA (Amazonian [manatee] rescue centre), and Quistococha Zoo are further out of the city on the same road that passes the airport. It seems quite straightforward to get a mototaxi and head down to either/both collection(s).
Guira Oga rescue centre and Biocentro, two separate collections in Puerto Iguazu in Argentina both seem like practical airport trips - again I think taxi is the easiest way, with a taxi costing less to the zoo than to the city centre. Bus is also an option, but involves a changeover in the city centre. Be wary of closing times (last tour is usually at least 1hr before closing).
Parque Das Aves, Brazil - Just across the border from Puerto Iguazu is Foz do Iguacu in Brazil. The road out to the Brazilian side of the Iguazu Falls goes out of the city for several kilometres before reaching Parque das Aves, the airport, and the falls quite close to each other. It's certainly very easy to cross over to the bird park from the airport but I'm not sure that visitors will be so keen to potentially miss out on seeing the falls.
