chocolatecoveredstrawberry: I second La Posada for Manuel Antonio. They are (or at least were) really budget-friendly but was actually the place I wanted to stay even without regard to budget. The place is beautiful and it is right outside of the park exit. You can walk to the beach and the park entrance–in fact, it was on this walk that the squirrel monkeys would come out and play. You aren’t limited by a cab unless you want to go up the hill, which we did to go to dinner a few times and to a spa. Definitely do a guided tour while you are there–it’s worth the money because you will see so much more and the guide will use binoculars to set up your camera. And I totally agree that Si Como No isn’t worth the hype–the food was okay but not the worth the effort or $$ and the spa was beautiful but the services not.
For La Fortuna, I also second at least going to Tabacon. It’s gorgeous during the day and gorgeous in a completely different way during the night. A lot of people say it’s overrated, but I’m not one. I like it better at night because it’s less crowded. Staying there is a trade-off. I think there are much better places for the money, but you do get free entrance into their hot springs if you are guest (and they have great breakfasts). My favorite thing to do there is the canyoning.
You said you were scared of heights so ziplines would not be enjoyable, but for some reason, at least for me, canyoning was different. I’ve done ziplining a lot and I have no idea why because i hate because of the heights! But canyoning was awesome. In La Fortuna the canyoning starts with a couple of drops which could be scary (but felt entirely different from ziplining) and the rest isn’t a lot heights (but it is very wet). I keep planning to jump down for a weekend to do it again and so my Fiance can see the volcano, but I do believe the volcano isn’t pumping out the lava. If it has/does start again, this is definitely something to see. I didn’t want to stay at the hotel that faced the majority of the lava flow at the time (it was too remote), so I hired a taxi to take me to that hotel, ate dinner there overlooking the volcano which was nice enough to erupt the entire time, and then take me back down. If it starts again, I’d recommend doing something similar because it is magnificent!
If you choose to add a third location, I again agree with the others—Samara or Monteverde. I think Monteverde is the typical add on for your itinerary because it’s close and it gives you a good feel of everything that Costa Rica has to offer. I haven’t been but people really love it (I always get pulled away by beaches and turtles). You’ll save time on transfers and if you are looking at going with a pre-planned tour, this would be common. If it were me, I would go to Samara.
Driving is a pain and I’ve always avoided it. The public bus works well, is dirt cheap, but not exactly comfortable. Private transfers rock but are expensive. Flying is nice because it is super fast, but it is really expensive, really really limits your packing ability (I have special CR bags I had to buy for flying because the weight and size limits are soooo small), and they cancel a fair amount. Interbus is a good middle of the way to go to get places. It’s a shuttle that goes in between places throughout CR. It’s air-conditioned and comfortable. The times are set so its rigid. Grayline Tours also provides the same service.
If you take a late flight and end up having to stay in San Jose for a night, I’ve had good luck at both Casa Laurin and Adventure Inn. It’s pretty simple lodging, but nice enough, clean, good people. Adventure Inn has kitchen. I had a really late plane one time, got there after the kitchen closed, and they made me dinner anyway. Both places have great people and are safe.