Both options will get you to central Guayaquil in about 20 minutes. The difference comes down to how much uncertainty you are willing to deal with after a flight.
The airport taxi system
Guayaquil airport runs a regulated taxi counter inside the arrivals hall. You walk up, state your destination, pay a fixed fare ($5-8 to downtown), and get assigned a registered driver. This removes the haggling that plagues taxis elsewhere in Latin America. The cars are generally clean but basic — mostly compact sedans. Air conditioning works in most but not all. Drivers speak limited English.
The system works well during the day when flights are frequent and taxis are plentiful. The main downside is that during busy periods you may wait 10-15 minutes for an available car, and the vehicles are not large enough for groups with heavy luggage.
Pre-booked private transfers
A private transfer means your driver is already waiting when you walk out. They will hold a sign with your name, help with luggage, and drive you directly to your accommodation. Vehicles are newer and better maintained — usually mid-size sedans or minivans. English-speaking drivers are standard with most transfer companies.
The cost is $15-30 for a sedan, which is roughly 3-4 times the taxi fare. For that premium, you get certainty: no waiting, no language issues, no wondering if the car will fit your bags.
Safety comparison
Guayaquil has legitimate safety concerns, particularly at night. The airport taxi counter system is one of the safer options — drivers are registered and tracked. However, a pre-booked transfer from a reputable company offers an additional layer of accountability since the booking creates a documented record of your trip.
Avoid unmarked taxis or anyone approaching you inside the terminal offering rides. This is a common scam vector at GYE.
When to choose which
Take the airport taxi if you are arriving during daytime, traveling light, heading to a well-known central hotel, and want to keep costs low.
Book a private transfer if you are arriving late at night, have children or heavy luggage, are heading to a destination outside the city center, or simply want the easiest possible arrival experience.
For solo travelers on a budget during daylight hours, the taxi counter is perfectly fine. For everyone else, the peace of mind from a pre-booked transfer is usually worth the extra $10-20.