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