What are the best ways to treat a deep muscle bruise?

See below. Massage, and alternating ice and heat.
Heat, rest. Heat, rest, and inti-inflammatories are your best bet for a muscle bruise. Also, avoid activities that aggravate the injury. You can then gradually advance your activities as the pain allows. If it does not get better, you can consider physical therapy for stretching and modalities such as ultrasound (heat therapy).