All vehicles rented at the San Jose (or Liberia airport in Guanacaste) have a 13% airport fee attached. That used to be the sales tax but changed to airport fee, plus the Value Added Tax (VAT) when went into effect last July.
Thus, a vehicle rented at the airport has a 13% airport fee and a 13% VAT. However, on vehicles rented not at the airport you pay only the 13% VAT.
Hah, but there is more. No rental car agency actually has vehicles at the San Jose airport, they are all at their “airport” office, which is the office nearest the airport. From the airport, you are taken by shuttle, which can be up to a few kilometers, to the office where you will then get your car with the airport fee applied.
However, if you first go to your hotel, get online, reserve your vehicle – do not use the airport location, rather the nearer office near your hotel – and you will get the same car but without the airport fee, only the value-added tax.
Or you can call or check with your hotel front desk for car rentals. Some hotels have car rental desks.
The disadvantage of renting at the airport is clearly the additional tax. On a week’s rental, the 13% airport fee can add up. For example, on a Toyota Corolla, with the full coverage can run you about US$150 a day or more (ouch) during peak season (like right now Christmas and New Years), the 13% airport fee is US$19.50 a day or US$136.50 a week.
Off-peak season price for the Corolla, with the VAT is about US$80 a day for the full coverage (is not insurance and not mandatory), in which the rental car company will assume responsibility for the loss of or damage to the car and usually requires a deposit of US$500, rather than the US$2,000 or US$3,000 on your credit card for lower coverages.
Note that the full coverage in many cases, at least in the case of economy cars, the amount is higher than the base rental of the vehicle.
A couple of examples of non-airport rentals.
At Avis, the base rate for a Nissan Sentra is US$36 a day (for January 6, 2020), the LDW is US$29.99. With taxes, the total daily rental is US$78.12. The same car would be US$88.27 at the airport.
At National, the base rate for a Toyota Corolla is US$31.90 (for January 6, 2020), the ‘maximum coverage’ is US$45 for the class of vehicle, with tax the total rental is US$89.04. The same car would be US$96.64 at the airport.