I don't think that's easy to say, every species contains subspecies, and even they contain individual differences in alkaloid contains. But the main alkaloid remains mescaline and others ranging only from 1-10%, I know one of them makes you very sleepy. I think differences are only very subtile if they are there. The facts seems to show that they both have potencies in the same range but it seems peruvian is easier to grow.
Another interesting cactus is the Trichocereus bridgesii, I didn't read a lot a bout even from Goran but this also seems to be a very potent cactus.