Although it is not an apart-hotel, I always stay at Fata Morgana when budget is the main concern. Very moderate pricing with basic but clean rooms. Maybe someone can give you a specific apart-hotel recommendation.
At Los Pueblos de Las Pescadores there is a restaurant called El Pescadore, just opened about 6 months ago, they also rent rooms behind the restaurant. The price is $40.00 per day. This is a good location and safe.
