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
Open Emacs.app from within Terminal.app (instead of from Finder):
$ emacs
This works for me using Emacs from Homebrew with Cocoa (brew install emacs --with-cocoa). It launches Emacs.app in a Cocoa GUI window (use emacs -nw to fallback to terminal UI). All the environment variables I have set in my bash environment appeared to be set in Emacs.
I have not tried this with Emacsformacosx. I personally prefer Emacs from Homebrew as I heard Emacsformacosx is not compiled with certain extensions I use such as TLS and Imagemagick... you can compile Emacs with those extensions using brew install emacs --with-XXX.