What about the American Empire of New England, run since 1684 by the Mather dynasty?
Founded in the wake of the abusive Dominion of New England, the AENE, which expanded to control most of Canada and land north of Maryland certainly is thought of as a theocracy, expecially considering that the Mathers are not only the heads of state, but also the heads of the American Reformed Church (founded in 1739 as a response to the so-called Great Awakening rippling through Britain). Also, when you recall the violence towards opposition to the Mathers and the ARC, such as the executions of Timothy Dwight (who wanted to change the ARC in 1780s) and Joseph Smith (who tried to create an opposition church in the 1800s), you can see why some call the AENE the most brutal theocracy in the world. Still, in modern times, the AENE has at least allowed its citizens freedom of speech, if not freedom to practice another religion.