The answer seems to be that Greene played so fast and loose with biology that there's no point trying to make sense of it. "Nemiphar" is indeed (probably) the water lily, but the connection with protection from electric rays appears to be something Greene made up out of whole cloth.
In Carmine G. di Blase's chapter "Euphuism and the Uses of Falseness" in Trompe(-)l'oeil: imitation and falsification by Philippe Romanski and Aïssatou Sy-Wonyu is an analysis of Greene and other writers of the period by someone who seems to know what they're talking about
Greene took the greatest liberties, however, with natural philosophy. The vast majority of these references - and this is a telling fact - would suggest Pliny as a source, but nearly all of them have been falsified to one degree or another. It will suffice here to characterize, rather than to list, the numerous falsifications that were revealed in annotating Gwydonius alone. It must be said, first of all, that Greene seems never to have studied Pliny at all. As Don Cameron Allen has shown, "the index to Pliny supplies many names, but Pliny does not supply the matter" [Allen 1007]. For example, when Greene says, "He that will fish for the torpedo must anoint his hand with the oil of nemiphar, lest he be charmed" [Gwydonius 88], he very likely is appropriating the names from Pliny but happily inventing the properties. Pliny mentions the torpedo, or electric-ray, quite often [Pliny IX. 24, 40, 67, 74; XXXII. 2, 31, 32, 33, 46, 47, 49, 53], but never any herbs that might prevent a fisherman from being "charmed" by it. And by "nemiphar" Greene might mean Pliny's nymphaea, or nuphar luteum (the white lily), which is mentioned in the Natural History over a dozen times but never with the property Greene attributes to it [Pliny XXV. 37, 83; XXVI. 18, 28, 36, 48, 49, 61, 83, 87, 90, 92].