Where in a thesis should a glossary be positioned?

I suggest to follow the order reported on Wikipedia – Book design.

Here is the suggested order (skip all that is not needed in your thesis; colophons are only needed in published works, and your publisher will take care of them):

• front matter
  • title page
  • colophon
  • contents
  • foreword
  • preface
  • acknowledgment
  • introduction
  • dedication
  • prologue
• body matter
  • content – optionally divided into volumes, books, parts, chapters, sections
• back matter
  • epilogue
  • outro
  • afterword
  • conclusion
  • postscript
  • appendix
  • glossary
  • bibliography
  • index
  • colophon

It is utterly a matter of style. Just put it where it makes more sense to you. If you expect people actually NEED to read it before they can read your thesis, just put it in front. Otherwise, put it after the main text.

Put the glossary after any appendices and before the index.

EDIT: This advice is simply based on a very quick survey of the textbooks that I had close to hand. The sample size is therefore small, possibly subject biased (physics, mathematics, astronomy, economics), and therefore subject to argument. Thanks to aeismail for the comment prompting this edit.