Middle English prikke, from Old English prica (n.) "point, puncture; particle, small portion of space or time," common Proto-Germanic (compare Low German prik "point," Middle Dutch prick, Dutch prik, Swedish prick "point, dot"). Meaning "pointed weapon, dagger" is first attested 1550s.
Earliest recorded use for "penis" is 1590s (Shakespeare puns upon it). My prick was used 16c.-17c. as a term of endearment by "immodest maids" for their boyfriends. As a term of abuse, it is attested by 1929. Prick-teaser attested from 1958. The use in kick against the pricks (Acts ix.5, first in the translation of 1382) probably is from sense of "a goad for oxen" (mid-14c.), which made it a plausible translation of Latin stimulus; advorsum stimulum calces was proverbial in Latin.