If you're spending any amount of time, LIR is on the Pacific coast. There are loads of activities there including great diving (don't forget your 24h wait before flying). I did a great dive there at the Bat Islands where there were quite a few mantas and bull sharks. Worth note though, the beaches there are volcanic sand, it's not the beautiful white sand coastline of the Caribbean side. The Pacific also tends to be significantly colder for swimming.

SJO is more or less in the middle of the country and a sizable city. Great if you're looking for a city escape, but I found it fairly unexciting.

For just the purposes of going just to use up North America segments, I'd easily chose LIR over SJO but I'd stay at least a few days to get a chance to actually enjoy it.