The facilities at Metropolitan Pool are by no means the best, but with a $75 a year membership I gave it a "great" rating.
The pool itself is clean, kick boards are available and there's a locker room with showers. Co-ed lap swimming is scheduled in the evenings, with women only lap swimming and kid's hours throughout the day. There are also swim lessons available every summer.
The gym equipment is basic - machines and free weights in one room, treadmills, bikes and elliptical machines in another - but again, for $75 a year you really can't go wrong. And I've never had to wait too long for the equipment.
NYC Parks and Recreation Gyms are located all over the city, and the membership for facilities without pools is only $50 a year.