In Costa Rica go to the Arenal area and to the west coast. Easy to drive around, safe, beautiful. Also flying into Liberia was very easy, its a good alternative option to San Jose. However if you go into San Jose, we stayed here - very reasonable, esp with kids: https://www.adventure-inn.com/

http://www.arenalobservatorylodge.com/index.php this place is right by the volcano and you can watch the volcano steaming and do some hikes. One night it starting spewing red lava which was rolling down the hill --- pretty awesome experience.

In the same area, this is a great place to spend a few hours one night in the world famous hotpools but dont do the dinner: http://www.tabacon.com/

Also in the same area, for a 650 feet in the air ziplines that are really fun: http://www.skyadventures.travel/Arenal_En/Welcome.html

For a different thing, rappelling down the face of waterfalls, we had fun here: This was pretty fun: https://www.puretrek.com/ - but not with a 2 year old so somebody would have to babysit.

Finally, This place has a fun water park that our kids enjoyed - you can do it without staying there, just buy a day pass, or if you're willing to drop more serious cash its a high end resort. http://www.thespringscostarica.com/

In a different part of the country, Manual Antonio is an area which is on most places as a must see, and is pretty awesome national park - my kids loved all the monkeys and other animals. Some listings for places there: https://www.vrbo.com/results/central-america/costa-rica/puntarenas/manuel-antonio-area/manuel-antonio This was a very reasonable place, clean, not overly fancy but good with kids: http://www.costaricavillas.com/villas/azul.shtml We also did a sailboat day trip with snorkeling - good for kids.

In the Manual Antonioa area, LA Selvita canopy tour - these guys were great with kids: http://www.laselvita.com/ing-secc_selvita.htm

We don't travel and stay in 5 star places - we like casual, clean, comfortable, and we're independent travelers so we rent a van and do our own driving - felt very comfortable doing so in CR. For a resort type place that was a few hours away from Jaco and Manual Antonio and nearer the Liberia airport, a very laid back, quiet place we stayed here, it was clean, and right on beach: http://www.tripadvisor.com/Hotel_Review-g635535-d580778-Reviews-Casa_Conde_del_Mar_Hotel_and_Resort-Gulf_of_Papagayo_Province_of_Guanacaste.html

Anyway, thats quite a few ideas, hope some help!