Hotel Mercurio
www.hotel-mercurio.com is a good choice right in the Old Town with more upscale rooms, a nice pool and a buffet breakfast each morning. The Vallarta Cora
www.vallartacora.com is less expensive option with more basic rooms and a daily Happy Hour/Tea Dance around the Pool, Hot Tub, Steam Room etc.
I've stayed at Torre Malibu and the units on the upper floors have great views and some of the units have been renovated so they would have nicer bathrooms, furniture etc. I personally found the smallish, internal bedroom that most of the units have a bit claustrophobic. They also have larger units in a separate building across the street.
If renting a condo interests you
www.pvrpv.com has a large inventory in a variety of price ranges. I'd stick to the "Old Town" or "Los Muertos Beach" areas if you want to be close to the gay clubs, restaurants etc. "Amapas" and "Alta Vista" are also nearby but further up the hill. Selva Romantica and Rincon del Almendro are the newest, most upscale buildings.