That's because she didn't say it. Dawkins's review of Sokal and Bricmont includes an unattributed reference to "a notorious feminist description of Newton's Principia (a 'rape manual')," alongside his discussion of Irigaray. The reference is to Sandra Harding's _The Science Question in Feminism_, in which she doesn't actually call the Principia a rape manual. Harding argues that philosophers of science have been inconsistent in saying that metaphors of domination and rape in early-modern science are irrelevant, at the same time as they treat a move to mechanical metaphors as being an important advance. The paragraph that concludes with the mention of "Newton's rape manual" reads:
"Traditional historians and philosophers of science have said that these metaphors [of rape and torture] are irrelevant to the _real_ meanings and referents of scientific concepts held by those who used them and the public for whom they wrote. But when it comes to regarding nature as a machine, they have quite a different analysis: here, we are told, the metaphor provides the interpretations of Newton's mathematical laws: it directs inquirers to fruitful ways to apply his theory and suggests the appropriate methods of inquiry and the kind of metaphysics the new theory supports. But if we are to believe that mechanistic metaphors were a fundamental component of the explanations the new science provided, why should we believe that the gender metaphors were not? A consistent analysis would lead to the conclusion that understanding nature as a woman indifferent to or even welcoming rape was equally fundamental to the interpretations of these new conceptions of nature and inquiry. Presumably these metaphors, too, had fruitful pragmatic, methodological, and metaphysical consequences for science. In that case, why is it not as illuminating and honest to refer to Newton's laws as 'Newton's rape manual' as it is to call them 'Newton's mechanics'?" (113)
Which is obviously debatable, but it's not ludicrous in the way that Dawkins suggests. Probably, he hasn't read Harding; certainly, that review of Sokal and Bricmont is an extended demonstration of Dawkins's ignorance.