Honestly I think that both are extremely useful for building muscle *as enhancement to a muscle-building resistance-training program*.
Yoga helps with flexibility, join mobility, strength relative to body size, breath awareness, energy, and body awareness. All of these things will aid in any athletic endeavour, AND it promotes relaxation and stress reduction.
Pilates focuses more on the "core" muscles - abdominals, hip flexors, back & gluteals - which allows you to lift more, more safely in a weight-training program, improves posture and alignment (which yoga may too), and (IME) is more of a "workout". It can also really help with specific areas of weakness, and I've always found I feel awesome after a class. It's great just from the "OMG I have abs and they feel FABULOUS" aspect.
Both types of exercise are best done in a class, which helps provide motivation and structure, as well as a social element that many people find helpful. Both types of exercise will build *some* muscle and strengthen and condition existing muscles, and are DEFINITELY better than doing nothing at all, but if you really want to lose fat and build muscle, resistance training is the way to go (along with interval training for cardiovascular/aerobic health).