I think that the only difference between the two is the semantic objective of the definition. Naturalism (see the [SEP](http://plato.stanford.edu/entries/naturalism/)) 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](http://en.wikipedia.org/wiki/Materialism) is the related view that all existence is matter, that only matter is real, and so that there is no metaphysical world. 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 materialism takes a premise (effectively that of materialism) to make an argument on how science/philosophy should function.