My favorite for years, until one of us messed it up and made it chica unfriendly about 5 years ago, was Aparthotel LaSabana, a few blocks from the park on a quiet street. Spotless, kitchenettes, free good bk, computer, fax, pool, sauna, coin laundry, free secured parking/free airport shuttle, lots of restaurants very near including fast food. If you're going to the west coast, a great jump off location.
Local Chinese owned since it opened in the 90's but completely Tico run. Looking at their website pics today, I see Luis is still the front desk manager. That's a good sign to me when a place has long standing managment in place. The DelRey being the exception re: "her" who's run more gringo's out of the DR over bar bill/hotel charges/lack of basic courtesy disputes then have 200 overly pesty gorda DR putas in the past year alone. Go figure, every one has their opinion on that one, mine is a big fat ass who sits at a desk 10' from her with a big smile on his face whenever he wants it. Not to mention popular bartenders who "disappear".
Aparthotel LaSabana is as quiet as you're going to get in SJ, a premium for me,
at those rates if you get a pool side room facing the front desk/kitchen, not in the wing above the front desk/kitchen, and not one facing the "backyard" so to speak which is a police car junk yard, at least it was. And now with a $11 for 2 hours at Queens hotel a block from the Rey first mentioned by Rac, it's a very nice out of the gulch option. Very very good rates for a really nice place close to the gulch (weekly discount rate too) for the smaller rooms and very moderate rates (weekly discount rate too) for the kitchenettes, check the website, offers storage at no charge though I didn't see it on their site but I know they do. Very well run place. Won't you need your laptop?
http://www.apartotel-lasabana.com/en/rooms/ratesAnother popular one is Aparthotel Christina,
http://www.apartotelcristina.com/ same general area by the Sabannah Park, never been there. Know guys that have and rave and last time I heard they weren't blocking a discreet entrance with a discreet chica. I did also hear $5 in advance to the guy you know will be working the desk really greased it.
Another cheaper option is Aparthotel El Sesteo, same general area, no where near as nice as the two above, has a website