First, why go to Manual Antonio? Its is a small park, a very developed and touristy area. You can hike the park in 2 hours all trails, the beach is small.
Why not go to Tenerio/Celeste Waterfalls, or Cano Negro, far prettier, few tourist, and lot ore wildlife and nature/beauty.
Arenal is not active either...
How many days do you have in CR? Are you going to caribe side? Tortuguero, Cahuita and Pt Viejo areas are all far more wildlife and nature, more rustic, and no car needed, all boats and buses and rent a bicycle.
That said, both are fine. I am pretty sure you will connect on those flights thru San Jose, it is not direct. Nature Air is twin engine Osprey, and Sansa is singe engine commercial Sesna's...
There is a shuttle between those two areas too...Interbus is good.
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