Sure Paradores are an option but I don't believe we have any in the San Juan area.. plus I would only recommend paradores, as you say, if you really wanted to rough it .

My suggestion is merely to search the classified ads in the newspaper to see what comes up. Many apartments are rented on a daily/weekly/monthly basis, but I haven't seen a good way to search for those (other than the classifieds).

PS. Can't believe you had that bad experience at the ESJ... Last time I was there, it was great...