I think you can only fly into San Jose, at least when I went. I went two years in a row for surf trips when I was 15 and 16. Since thats all we did thats all I can help you with.
I would definately recommend Jaco and Playa Hermosa, its gorgeous, right on the beach, and the only drawback (which is also a plus) is that it is very 'Americanized.' I wouldn't stay there the whole time but its worth checking out and the zipline tour they do out of the Hotel at Playa Hermosa is amazing, your in the tree canopy overlooking the Pacific.
We also went down South to the Panama Border, Pavones to be exact. That was my favorite part of the trip both years, going to Pavones and Dominica. Both were a little 'rugid' for a honeymoon, but I guess it depends on your partner.
Congrats by the way. Pavones is a short drive to Bocas Del Torro and if the drive is too far there is alot to see right behind the hotel, we got robbed by spider monkeys
and saw plenty of Macaws in the afternoon. If your in Pavones and see a long hair guy driving a Bronco tell him I said whatsup, he's my old boss.
I've never been to the Caribean side but if your down by Pavones its not too far of a drive.
The waves are alot better during our summer (their winter) but I doubt you'll get skunked in the deptartment. I have a book and all the numbers to these places if your interested.