While both have their uses (see below), the experts (such as WebMD and Mayo Clinic) suggest only icing in the case of Chondromalacia patella . The Stretching Institute actually advises not to use heat 24 to 72 hours after an injury. Because of these articles, I would use ice only, unless told otherwise by my doctor.
Ice after a run will help relieve swelling and pain.
Heat helps increase blood circulation, bringing additional oxygen and nutrients. In general, heat has been recommended before a workout to loosen the localized area, and before bed to increase blood flow, which brings additional oxygen and nutrients to the localized area.
Other advice included rest, elevation, compression, aspirin, and of course, seeking appropriate medical treatment.