Working with emacs in OSX can some times be troubling.
I interchange with using the Terminal.app application and the emace shell both of these use bash, and
If your environment variables are being set in ~/.bash_profile, Create a file called ~/.emacs_bash and put in it the following:
. ~/.bash_profile
Don't forget the newline at the end of that line or it won't be executed.
~/.emacs_bash is loaded by emacs when you run bash from within it, such as when using M-x shell or shell-command so you can use it to set any environment variables you want available.