I need to get dental work and the closest hotel with a good room rate was the Santo Tomas. It was rated as a 3 star and my experience is whatever the stars, they're usually less - Marriott 5 stars to me rate 3 or 4 at best. Other hotels, and I've been in at least 30 of them in Panama and Costa Rica, rarely meet my expectations.
I'm spoiled and like to be spoiled.
First, the owner is at the hotel almost every day assuring that each guest is accommodated and feels like a guest, instead of a mark. Every employee of the hotel was pleasant, although the room only had a queen bed, I was apprised of this beforehand and the bed was fairly comfortable, the room was a nice size and the shower was excellent. Give me a comfortable bed and a great shower, nice hotel employees and I am usually satisfied.
Here the employees went out of their way (or maybe it is their way) to make me feel welcome and glad to be on the property.
There's a gym to work out in, which I loved, a swimming pool, a Jacuzzi, and last but not least, a coffee machine in the lobby that makes better coffee than any place in town - and this is Costa Rica, the country that makes great coffee.
If you're looking for a very clean, comfortable place to stay in San Jose, at a rate that is very reasonable, this is the place. I'll be back, as I visit Central America 3-5 times a year and LOVE San Jose.

We were using San Jose as a pass through to Manzanillo on the Caribbean coast. We arrived and got to Santos Tomas late in the evening. The person at the desk lead us to a nice quiet room. The room was in a part of the hotel that is one of the older homes, it was nice, clean and happily quiet. Breakfast the next morning was an excellent Gallo Pinto with salsa ingles and toast. The hotel was very nice on the inside, something you would not know from the exterior. The owner stopped by during breakfast and chatted amicably with all those in the dining area. He was a warm, US expat.

For the return trip we were dropped off by our shuttle at 6:30 pm and shown to a room in the new upper floor. Very nice. The view from the balcony was great, overlooking the courtyard and pool. We decided to eat at the Oasis, the in-house restaurant. There was not much for us Vegans to choose from, but Carlos, the only person visibile, came up with a blend of vegetables in the house pomidoro sauce over pasta. It was tasty and fit the bill for us. The staff was excellent and very professional. If I need a hotel in San Jose again, i will certainly see if Santo Tomas is available.

Not a cookie cutter hotel. Lots of outdoor spaces attractively sited around a landscaped pool area. Our large room overlooking a second floor outdoor seating area had comfortable beds, spacious modern bath, and charm. Staff was friendly and helpful. Breakfast was freshly prepared. We enjoyed the convenient location in walking distance to downtown San Jose and major museums. We would definitely return and would recommend the hotel to others. The art, ironwork and ambiance make this place a distinct contrast to chain hotels.

We have stayed in San Jose before. In fact this is our third trip to Costa Rica. I can honestly say that this is the best hotel that we have stayed at in San Jose. The hotel staff was very helpful and our room was clean and comfortable. I would definitely stay there again.