I always suggest going straight to Jaco and staying at Mango Mar or the bare-bones Cadillac Rock. Arriving at midnight, you should be in Jaco by 2am, early enough there should still be some "fun" hanging out at Orange Pub or Le Loft. And personally, I love driving at night...little traffic so an easier and quicker trip.
But for cheap hotels close to the airport, my first recommendation is Dos Palmas
http://www.dospalmascr.com/airport/en/index.htmAnd for airline cost, you might also check out Southwest but they too arrive around midnight...