A lot of very good advice here. Of those mentioned here, I've stayed at the Don Carlos, Casa Conde and the Best Western Irazu. They all have different things going for them. Do you plan on trying to slip away for a little action? Then braving the little seaminess that exists downtown may be a small compromize for being able to easily pop out for a walk and then making a quick run to one of the MP's. OTOH, as TMan pointed out, if there are young K*ds in your family, you may be more concerned with security and prefer someplace a little safer (also I didn't think any downtown hotel had a pool which your K*ds might want).
Don Carlos is very quaint and cozy B&B type place and the neighborhood is close to the gulch but not in it. In fact one of the times I stayed there was with my family and they all loved it. It is directly across the street from the New Fantasy so be sure they don't get rooms on that side of the hotel if you plan on popping in there. Last time, I was there I had room #10 which was very nice but had a direct view of the front door to NF. The exit for the hotel is on another street so your family may not even notice NF is there.
I haven't stayed at the Amon but it is just a little further away in a similar neighborhood, no pool for the K*ds but a casino for the adults and just one block from Zona Blue for you. I haven't stayed at the Holiday Inn either but it is directly across the park from the Key Largo (ie very close to the Gulch) and IMHO seems to be kinda pricey for what you get compared to those other hotels. Furthest out of any of what could still be called downtown hotels is the Tournon. It is few blocks north of the Amon and almost directly across the street from El Pueblo, a quaint and popular little mall with shops, restaurants and later at night very popular bars (just be careful about the gunfire- ask megustachicas
). I didn't realize they had a pool
My first visit to CR I stayed at the Best Western Irazu. It is on the way into town from the airport and the furthest from downtown of all the hotels mentioned. It is definitely no B&B and has the US-style standardized hotel rooms which you might prefer (as does the downtown Holiday Inn and Amon Clarion) and a Denny's if CR food is not your cup of tea. It also has a good sized pool which I never used. If you plan to rent a car or if you plan to use it as a base for exploring the central valley and the rest of CR it is not a bad choice as you will be able to avoid a lot of the downtown traffic. The Sabana Park area hotels are much closer to downtown without being in it and may also make a decent compromise trafficwise.
As for Casa Conde it is very nice (again stayed there with family and they loved it) and with the CRT discount can be a very good deal since the accomodations are shared. I'm not sure if they have 3 bedroom apartments, but with a 2 bedroom you might come out much cheaper than you would on 2 regular hotel rooms downtown that aren't nearly as nice. Their suites feature full kitchens, their own laundry machines, stereo, a good sized TV w/cable and even jacuzzis in some of the suites. They also have a small pool. It is outside of downtown along the highway that circles the city, but being on the south end of town near the mountains is not as close to any of the more common exit points along the PanAmerican Hwy to the east and west of the city or even the Tibas-Guapiles Hwy to the north that takes you to the Atlantic Coast, so traffic getting anywhere else can be a small problem. But that is the only real negative for that place.