Well my information is based on The Last Sorcerer, which identified 2 men who it seems likely that he had long-term relationships with.

As I recall the evidence boils down to Newton's censoring of some letters and two long-term relationships with John Wickins, his roommate from his Trinity days, and a young Swiss mathematician whose name escapes me.

Could he be gay? Certainly. Are there any number of alternate explanations? Yup.