We don't know that Newton had sex with anybody, whether male, female, animal, vegetable or mineral. Most biographies of the man simply don't deal with it much, as there's really nothing to go on. As far as anyone can really know, Newton was chaste.

In one of his writings on early church history, there's an oft quoted sentence in the middle of a long account of the asceticism of early monks, where Newton seems to voice a personal opinion on the matter:

The way to chastity is not to struggle directly with incontinent thoughts but to avert the thoughts by some imployment, or by reading, or meditating on other things, or by convers.

(The fact that it's often quoted may say more about how hard people have looked for evidence of Newton's sexuality, than the quote does about the sexuality itself)

Now, it's true Newton had a well-known mental breakdown of some sort in 1693, and the causes are much debated. There was an old apocryphal story (not unlike the apple one) about Newton's dog Diamond starting a fire by toppling a candle, and causing Newton's breakdown from having his papers burn up. This kind of thing was reported as fact in early 19th century biographies (e.g. those by Jean-Baptiste Biot, Walter Scott) A more modern theory is the neurological effects of heavy metal poisoning and there's some forensic evidence to support that, another is the deterioration of his friendship with Nicolas Fatio de Duillier, which is probably what these gay rumors are about. Anyway, to quote the summary in Gleick's biography at length:

The particulars of Newton’s breakdown will forever inspire debate and speculation. As for the fire, most believe Newton lost some papers to fire in the late seventies; Westfall goes further and suggests, “There may ... have been a fire—another fire, as it appears to me—which could well have distracted him when he was already in a state of acute tension. Charred papers survive from the 1690s, though it is difficult to fit them....” Never at Rest, p. 538. A popular legend involving a dog called Diamond and a candle (cf. Bartlett’s Familiar Quotations) is surely apocryphal. [...] As for mercury poisoning: he did suffer symptoms such as insomnia and apparent paranoia, but he lacked others, and these were temporary; modern tests of his hair did reveal toxic mercury levels, but the hair cannot be dated. Some of the debate plays out in Spargo and Pounds, “Newton’s ‘Derangement of the Intellect’ ”; Johnson and Wolbarsht, “Mercury Poisoning: A Probable Cause of Isaac Newton’s Physical and Mental Ills”; Ditchburn, “Newton’s Illness of 1692–3”; and Klawans, Newton’s Madness. Whiteside has summarized the scholarly state of affairs: “Where scholars have, from the pedestals of their own stand-points, bickered ceaselessly this past century and a half over the possible causes and long-term after-effects of Newton’s undeniable breakdown ... we would be foolish to attempt any definitive assessments when the extant record offers but a blurred glimpse...” Math[ematical Papers] VII: xviii.

When it comes to Fatio, it was far from a lifelong friendship; they'd only met four years earlier in 1689. But Newton was indeed very fond of the young man. Apart from the fact that Newton liked this young protege I'm not sure how one would infer a sexual relationship. Newton bunking at his place when he was down in London for a week? (Letter of October 10th 1689, Correspondence of Newton, #346) Not really very eyebrow raising. More imagination-inspiring is the fact that the same letter has words cut out in three different places. Censoring personal secrets? It's not obvious what the missing words might've been but one of the lacunae is in the middle of a sentence where Newton is explaining his dislike for Robert Boyle. So that would speak against that theory.

Anyway at most all you really have is pure speculation. We don't know what Newton's contemporary colleague Robert Hooke looked like, so our chances of knowing what Newton did in the bedroom are probably slim. (ironically we do know that Hooke had sex though, despite never marrying)

(Additonal sources: James Gleick, Isaac Newton, 2003. Higgitt: Recreating Newton, 2007)