It's really up to you and what you prefer to do.
Yes, you can go to Ostional in the afternoon and see plenty of turtles. However, if you want to do so, make sure you enquire locally what the situation is. Sometimes, there are thousands of turtles, sometimes just a few.
The drive back is alright although you will likely have to cross a few rivers - thus, make sure you know what you are doing and where you are going. Things can look fundamentally different in the dark.
Mal Pais/Santa Theresa would require that you leave early in the morning in order to make it worthwhile - otherwise you are going to spend a lot of time driving and not enjoying the area.
Barra Honda is roughly an hour from Samara (could be up to 1 1/2 hours depending on conditions and how well you find the road). Generally speaking, I find it alright to be at the park around noon or so. That still gives me plenty of time to hike up and go down into the caves with the ranger and still make it back to Nicoya before dark. From there, it's an easy drive back to Samara.
There are some tour operators that offer boat tours of the Tempisque. However, I have never used one and thus, can't really recommend one. I keep seeing one just a few miles from the bridge, but I don't remember their name or what they specifically offer.
You could also contact some of the local operators and see what they offer: