Is the male bee's penis homologous to the female bee's stinger?
After a little bit of digging I was able to find a couple of facts that seem to verify that the drone bee's penis is in fact homologous to the worker bee's stinger:

This Wikipedia article about the stinger that says a honey bee's stinger is "a modified ovipositor as in other stinging Hymenoptera".

This book (actually about soil arthropods) states very specifically that, "The ovipositor, with which the female lays her eggs, is homologous to the male's penis.".