It seems to me any pirates on the Great Lakes are going to gave some geographical obstacles--passages between the lakes are comparatively narrow, and it seems like those chokepoints could be kept under control even by fairly weak government presence, at least once the already is developed enough for there to be much of anything worth pirating. There were forts on the Straits of Mackinac as early as the Seven Years' War OTL, and the Niagara and Detroit areas would be additional chokepoints. So pirates could have significant trouble moving from one lake to another, and I'm not sure that any one lake could support much of a pirate population.