The fact that I have seen so many comments about this on here terrifies me.
First of all, there is nothing wrong with your child. Gender exploration is normal. It has nothing to do with a parent of either gender being there or not - obviously, if lesbian couples can raise self-identified boys.
Second of all, if this is causing your child stress, there is a good chance it is not a phase. Transgender people often know from a wrong age that something is wrong and be self-destructive and antisocial if their problems are ignored or if they are told they are "wrong".
The fact that this has persisted for so long is a good indication that this is real. Instead of going to a pediatrician, go to an affirming psychologist who can help YOU understand what your child may be going through.
Besides, if your child does decide - without outside pressure - to change and express fully as male, what's the harm in allowing female expression now? If you never tell your child this is a negative thing, there will be no need for shame.
It's good that you are seeing your pediatrician about this. Does he watch you put on make-up? I don't let my 5 year old boy see me do this because then he wants to do that too. Maybe he admires you and wants to be just like you. Does he have a dad around?