The places mentioned thus far are all nice in their own ways but also all very different. What it comes down to is that you need to tell us more about what you are looking for. Do you want to be able to sneak off for some side action or is this really for you solely a non-monger trip? Do you want to be far enough away and removed from any action such that your wife does not figure out how much mongering goes on in CR and spoil future solo visits? Do you and your wife prefer more of the smaller individualized and charming B&B type hotels or the larger chain type hotels with more of the amenities and atmosphere of the US chains you're used to? What is your budget?
I'm afraid a lot of the opinions offered so far seem to be for places that are already popular on this board for mongering purposes. That doesn't mean that some of them wouldn't also be suitable for what your needs are. I'm just saying be aware of a possible bias filtering into the suggestions as result of where you posted this question. Generally tourism questions of this nature might be better asked on a different type of CR forum although you can also get good general tourism info here as well.
If this is a non-monger trip keeping your wife in the dark, then I'd avoid downtown hotels near the gulch such as Casa Vino, Don Carlos, Amon Plaza or the Aurola HI. Otherwise, of those, my own preference would be the Don Carlos, where I've stayed a few times. That and the Casa Vino are more of the B&B type hotel. The Casa Vino, I don't know much about. The word on the board is that it is nice and also chica friendly, which is a big part of why Dave probably likes it but which may not apply to your particular situation. Dave actually mongers WITH his wife (lucky stiff). Yours may not be so open-minded. If your goal is to limit the possibility of your wife being exposed to the sight of older gringos such as ourselves strolling into your hotel arm in arm with young chicas and giving her bad ideas of why you're so interested in CR, then that is far less likely to happen at a non-chica friendly place like the Don Carlos. The Amon is also nice from what I've seen but more of a chain style hotel. The HI is definitely part of a chain and has gotten reports for being run down though it was recently supposed to have been partially remodelled. Of those 2, I'd go with the Amon.
Getting out of the Gulch area, you become more removed from mongering action , which can be either bad or good. Get out of the city and into the surrounding valley you also become more removed from the traffic, smog and congestion of the city.
The Grano de Oro is very nice. It is in the Paseo Colon area on the west side of town. It is just a few blocks from Oasis, if you want to sneak away. But staying there or even going up the street for dinner at Machu Pichu, which is directly across from Oasis, your wife would never even realize Oasis was there. The downside? It is a little more expensive than the other places mentioned so far.
Hotel M is supposed to be very nice on the exact opposite side of downtown in the nice residential Barrio Dent neighborhood. I went to language school right next door, but the place is new and wasn't there yet when I was there (or at least I didn't know about it at the time). VB says you wouldn't know that it markets itself heavily to mongers but that is what it they do and its hard to believe you and your wife could stay there without her seeing what goes on. Also, it seems to also be on the pricey side for what you get although that is mitigated with the great CRT discount you can get there.
The last of the SJ hotels mentioned was the Casa Conde. It is in yet another direction from the city center on the south side of town. I've stayed there too and think it was very nice. It is a short cab ride into town but the area around it has a lot of traffic as it is just off of the auto-pista that encircles the city. And there is nothing else in the area that is really of much interes. The Casa Conde itself is in a quiet gated compound with several nice apartment style buildings. I'd recommend the Casa Conde if you wanted to make it a base for your extended stay in the SJ area with its kitchen and washer/dryer facilities in each apartment (also very nice stereo sound system, TV and jacuzzi).
Pesonally, if I was going to CR and didn't plan on doing any mongering I probably wouldn't even stay in the city let alone in the Gulch (particularly if you plan on renting a car). The city itself has at best 1 day of sightseeing in it. It does have nice restaurants but you can still come into town for that or avoid downtown and try one of the many nice ones that are also in Escazu. BTW, while I'm on the subject of restaurants, I recommend you go to one of the Mirador restaurants that are up in the hills overlooking the valley for one of your nights. The sparkling city lights are gorgeous from up there. If you stay at the Casa Conde than the Ram Luna in Aserri is your place but if you're staying elsewhere there are also several in the hills above Escazu.
I've stayed at the BW Irazu too and if you want a US chain hotel that is devoid of any character then the BW is your place. OTOH, its very affordable, has a nice pool (if thats your thing), casino, Denny's restaurant, has plenty of parking if you have a car and is right off of the highway leading into town from the airport.
I hope this helps you sort out some of the options mentioned thus far. However, just to confuse you further, I'll throw out one more suggestion on a place to stay and that is the Hotel Bougainvillea. It is in a nice natural setting just outside of town. They provide a free shuttle that will take you into town and drop you near El Pueblo (which has many nice restaurants and nightlife) or you can catch an inexpensive cab from ther and go anywher else in the city. So the place is good whether you have a car for getting out of the SJ area or whether you don't. Just another thought.
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