Nylon thread has a low heat tolerance (it will melt under high dryer heat), turns yellow over time and goes brittle. Poly has a higher heat tolerance (both will melt when pressed directly with a hot iron), does not turn yellow, nor brittle, with age. Poly is shinier. Choice depends on how you are going to use it and personal preference.
Two good sources of info:
http://www.superiorthreads.com/educa...nt-recommended
http://quiltbaggs.blogspot.com/2008/...polyester.html