My husband and I stayed at Si Como No for 2 nights in November 2006. It is a great place to stay with the kids due to the family pool with a really fun waterslide (yes, we liked it too) and a THX movie theater on the hotel grounds (XMen Three was showing while we were there). Also, make sure someone orders the banana flambe dessert, adults and kids really enjoy the presentation. Manuel Antonio park will be great for the kids, although you may have to carry the 3 yr old in some parts of the trails. You get really close to the monkeys, iguans, etc. I recommend a guide for your first trip to the park, as you will miss 80-90% of the wildlife without one. After that, you will know more what to look for and where it may be. The beaches inside the park are very nice...just take your own snacks & drinks, etc. 4 days should be good.
we also stayed at the Peace Lodge at La Paz Waterfall Gardens..Loved IT!!!! Stay 2 nights at least so you get more than one crammed day to enjoy the exhibits and grounds (kids will like catching a fish in the trout pond and feeding the hummingbirds, seeing the butterflies and frogs, etc.) Again, you will most definitely need to carry the 3 year old on the majority of the waterfall trails, but the views are worth it!!
Try the sky tram in Arenal...it is a good way to see the canopy and I don't think there is an age rescriction for it. Also, one of you and mabey the 7 yr old (not sure what age/size resctrictions are) could zip line down, while the others take the ride the sky tram back down.
I saw kids at the Tabacon Hot Springs, but none as young as 3...I don't think this is a good place for the kids (water quite hot, footing trecherous even for adults, currents in some pools quite strong), although a wonderful place for adults. Have fun and enjoy!!! This is a great country to visit.