In his paper On Newton and the Trinity in the Summer 1996 Biblical Astronomer, John Byl cites numerous secondary sources to show that Newton rejected the doctrine of the Trinity and embraced Arianism. Byl suggests the supporters of Newton's orthodoxy should consult primary sources if they wish to make their case. In fact, doing so should be easier than I once thought.
Some years ago, in a casual conversation with a historian of science whose specialty is Newton, I lamented the inaccessability of most of Newton's writings written in Latin and never published. Wrong and wrong, he told me. Other than the Principia, Newton wrote nearly everything in English in a flowing hand that is completely accessible to a modern reader. Moreover, his notebooks and unpublished manuscripts all are available in a well-indexed microfilm collection. The set isn't cheap, but many major research libraries (for example, the University of Minnesota) have it.