The caps tend to contain more psilocybin and psilocin than stems.
From Morphological and chemical analysis of magic mushrooms in Japan :
..... The psilocin/psilocybin contents in P. cubensis were in the range of 0.17–0.78%/0.44–1.35% in the cap and 0.09–0.30%/0.05–1.27% in the stem. Hallucinogenic alkaloids (psilocin and psilocybin) have a tendency to be contained in the cap more than the stem.
Our results are in agreement with the findings of Wurst et al.
 who found lower concentrations of psilocybin in the stem than in the cap of the hallucinogenic fungus, Psilocybe bohemica. P. cubensis samples also had a tendency to contain larger amounts of psilocybin than psilocin. This tendency is consistent with results reported by Bigwood and Beug
When the data from the above study is proecessed, it shows that in the samples of the above study, the caps were 30% more potent
Mushrooms though come with caps AND stems thus it would be a complete waste to only use the caps just because they are slightly more potent.