We will be making a similar trip around Thanksgiving. Flying into SJO and out of LIR. Because we will have a 4 year old with us, we are going to start our trip at the Peace Lodge which is an hour outside of SJO. It's a great place for kids to see and interact with all of the animals native to CR and I think Mr. Ericka and I are going to enjoy it, too! The lodge is set in a cloud forest with lots of waterfalls, etc. Perhaps your boys will be too old to appreciate it, but you should look it up anyway and see what you think.
We're doing 3 nights at the Peace Lodge and then 6 nights at the FS.