There are a number of options to get you to Manuel Antonio from San Jose. All are safe and reliable.
Of course the quickest option is a 20minute flight from the San Jose airport to Quepos/Manuel Antonio airport. You fly low in small planes with stunning views. there are flights about every hour but only during daylight hours as smaller airports in CR don't have night time runway lights. Two local airlines serve Quepos. The cost 1 way is around $80US.
Costa Rica has many shared and private van shuttle services from. Daily shuttle services run from San Jose to Jaco, Manuel Antonio, Dominical, Uvita, Sierpe, Arenal, Monteverde, Guancaste Beaches etc in modern vans A/C, professional drivers. PIck ups occur from various hotels in San Jose and in Manuel Antonio. The trip takes about 3 hours on an excellent and picturesque highway. We recommend 'Easy Ride Shuttle'. The cost is around $50US each way.
Another option is to rent a taxi from the airport - or ask your hotel to send a taxi to the airport. The normal cost is $125 to $150US and it takes about 2.5 to 3 hours on an excellent highway. Taxi's can be arranged with your hotel/rental villa concierge, or you can ask for one at the airport at the taxi booths.
Safe reliable public buses run every hour from Tracopa Station in central San Jose to Quepos/Manuel Antonio for about $10US.
The drive from San Jose to Quepos is 170 km and takes 2 1/2 hours, depending on the traffic. Expect a slow drive, the maximum speed limit in Costa RIca is 80km/hr. There are a wide variety of rental car companies. Basic liabiilty insurance is a must in Costa Rica. The basic liability insurance is not covered by credit card insurance companies, but your company likely will cover other types of liability - check with your company's policy and bring a copy.