Recently I have been reading the Tanya so that I can discuss Chabad Chassidus with my friend. I think it's only fair to see what the other side has to say, so is there any work that the mitnagdim published that I would have access to and could read? Alternatively, if there isn't, is there any work published that explains why some people don't follow Chabad Chassidus?
The most important misnaged was the Gaon of Vilna. The most substantial collection of his metaphysical teachings is his commentary on ספרא דצניעותא, which you can find here: http://www.hebrewbooks.org/24946
His two leading disciples were חיים מוולוז'ין and מנחם מנדל משקלוב. As mentioned in the comments, Nefesh HaHayyim, by the former, is a major work of misnagdic metaphysics, and is widely-available.
In the third generation, יצחק אייזיק חבר continued the work of his predecessors, forming the material into a comprehensive and systematic re-interpretation of עץ חיים. His work is called פתחי שערים and is available here: http://hebrewbooks.org/34671
In the fourth generation, the בעל הלשם continued this lineage and deepened it. The book of his that he meant to serve as an introduction to his teachings is called הקדמות ושערים and is available here: http://www.hebrewbooks.org/37238