Juan,
I have been to Guatemala and know what you mean, but keep in mind that Guatemala is a much poorer country and not nearly as popular on the tourist circuits, hence slightly lower prices. From the tone of your post and the fact that you will be travelling with your whole family, I am guessing you are economy minded.
I also have completed a family trip to CR this past Thanksgiving and so have an idea of what you may be looking for. In SJ, my recommendations would be the Hotel Don Carlos if you want to be in a nice family B&B that is still close to the Gulch for an occasional sneak away. If you would rather not chance it and would prefer to keep your family as far away from the monger action as possible (but still stay in the city), the Casa Conde would be a good choice with 2 bedroom suites featuring a kitchenette, in-room washer and dryer and a nice living room for not much more than a regular hotel room. It is located on the south side of town. If you prefer to be more outside the hustle and bustle of downtown SJ, some people would recommend the Best Western in Irazu (on the way from the airport). I have also stayed there and it is not bad, but I think it has more the feel of an American chain hotel (which you might like anyway). Personally, I prefer places with more local charm. Another place outside the city that I haven't stayed at but have seen good reviews on is the Hotel Bougainvillea. If you stay there let me know what you think.
In Arenal, the nicest choice is the Tabacon Resort. I know you said non-resort, but this place is nice and if you factor in the amount you would otherwise pay for admission to Hot Springs it is not really that much more than other area hotels (which tend to be getting pricier as the local tourist market booms). This would be your best place for your splurge. I usually stay just one night and try to get in hot spring sessions both days to really get my money's worth. I've also stayed at the Arenal Lodge but was not impressed. Another option that might be a little less expensive than Tabacon (and still have volcano views) is Hotel Montana de Fuego. You can also find more economical choices closer to La Fortuna but will probably not get a good view of the volcano if any.
For info on hotels and many other things in the Sta Elena area, you have to check out
http://www.monteverdeinfo.com. When I was there with my family, we stayed at the Hotel Belmar. It was very nice, but I couldn't swear it was the best value in town. There are certainly less expensive options. There was a recent thread on the subject of hotels in this area where I described a 2 night stay alternative that economized on the 2nd night and included a horseback, jeep and boat trip across the lake to Arenal.
There has been much said around here on beach hotel choices. I'll let you use your search feature for that. But let me say a few things. First if mongering is not a factor than Manuel Antonio is a MUCH nicer beach area than Jaco and is only 1 hour further along the coast. Guanacaste also has very nice beaches but may be too long a drive for your 7-10 day trip given all the other places you are already trying to squeeze in. Ultimately you might opt for Jaco just due to time constraints and should even consider not trying to squeeze in so much to your stay, though it certainly can be done