I think that the only difference between the two is the semantic objective of the definition. Naturalism (see the SEP) is the view that the world can be explained entirely by physical, natural phenomena/laws. Naturalists either assert that there is no supernatural (or metaphysical) existence, or that if there is, it has no impact on our physical world.
The branch called Ontological Naturalism focuses on how science can explain the world fully with physical laws. Methodological Naturalism focuses on the idea that philosophy and science share pursuits, and holds that any mention of the supernatural has no place in either philosophy or science.
Materialism is the related view that all existence is matter, that only matter is real, and so that there is no metaphysicalthe world is just physical. It simply describes a view on the nature of the universe, while the different branches of Naturalism focus on applications of effectively the same view.
Thus, the difference between the two is the purpose of the definition - materialism makes an argument about the ontology of the universe, while naturalism takes a premise (effectively that of materialism) to make an argument on how science/philosophy should function.