The first half of our trip was an all-inclusive package. We chose that since we wanted to go to Tortuguero, which is only accessible by boat or plane. It took a couple-hour boat ride to get to our resort - but you get to see a glimpse of how people live in the area. Tortuguero is in the rain forest, with monkeys right in the resort. It has amazing bio-diversity. You go on boat tours to spot the various wildlife, which is very abundant, and during the right season, you would be able to see the green sea turtle nest on the beach.
The second part of the package was Arenal Volcano - which can easily be done on your own. Arenal is an active volcano with Tabacon Hotsprings at the base. The hotsprings are a must-see. It's quite expensive but well worth it. It is a spectacular landscaping and setting. Apparently, across the road from the commercial hotspring is a natural hot spring which is much more reasonably priced but much more rustic.
After Arenal, we made our way back to San Jose - rented a car and headed out to Tamarindo. This is nice little town which will be the next hot spot. When we were there, a new large resort was being built, with a few more planned. It has a spectacular beach with hardly any people - it is a great place to go and eat breakfast, lunch, or dinner. There is small grocery store where you can purchase the items for your picnic. We kayaked out to the small island and had a guide with us to go snorkelling. It was a great experience, with him finding all kinds of neat things for us to touch and hold (blow fish, starfish, and a sea cucumber). We also had the opporunity to see a leatherback turtle nest. It was a once-in-a-lifetime opportunity which I would highly recommend - just remember that they are wild animals, and they are not posing there for you.
After Tamarindo, we headed to Poas Volcano - there is very little to no accommodations in the area, so plan your trip accordingly. The volcano is often clouded over, so pick your day carefully. In the area, we also went to Lapaz waterfall garden - they also have a butterfly garden, which was impressive to see. The last stop was Cafe Britt. They have a very informative tour and friendly staff - my only recommendation would be to buy your coffee in the grocery store, since it is significantly cheaper.
Costa Rica is a very ecologically diverse country, from rain forest to mountains to desert. It is a country that you can easily negotiate yourself, with very friendly people.