Manuel Márquez de León International Airport, La Paz: The sensible gateway if you are not committed to Los Cabos: it is the quieter airport and Todos Santos is roughly 60 minutes from La Paz itself. Pre-book a shared shuttle or private transfer, or rent a car at the airport; airport-to-town journeys commonly run about 1¼–1½ hours once the airport leg is included. A quoted low-cost route via La Paz is around MX$240, but it involves connections and is not the arrival-day choice with luggage. Use a confirmed shuttle/private quote rather than assuming an airport bus will line up with your flight.
Los Cabos International Airport, San José del Cabo: Use the scheduled airport bus/shuttle toward Todos Santos if its timetable fits: services are reported about every two hours, around 1 hour 45 minutes and roughly MX$200 one way. Otherwise, pre-book a shared shuttle or private transfer; private vehicles are commonly quoted around US$185–390 per car each way. Do not pay an on-the-spot airport taxi premium unless you have no alternative. SJD is farther and busier than La Paz, but often has better flight choices.