I would say the majority of psilocybin and psilocin are found in the stem. The cap only accounts for what 15% of the mass? I've grown albino Penis Envy and those stems were an inch thick and about twice as dense as the cap. I actually used a hack saw to cut them up into bite sized pieces and the pieces turned the darkest blue I've ever seen. Bluing stems indicated the oxidation of psilocybin, although not an indicator of relative potency, it certainly shows there is plenty of psilocybin and psilocin in the stem.
I've heard that the cap contains a slightly higher concentration of psilocybin from several people experienced with mushrooms, but not much variance to make it an issue. I feel that the individual genetics of each mushroom will have a far greater effect on potency. Levels of psilocybin and psilocin will vary unpredictably from one mushroom to another and one flush to the next when using a multi spore innoculation so I feel it is a generalization at the very least to say a cap is more potent then the stem.