Setting GUI-accessible environment variables in OSX is non-trivial, and environment variables set in standard places (like in your .bash_profile file) are not always available. The recommended process for setting them is described here: http://stackoverflow.com/questions/135688/setting-environment-variables-in-os-x
However, IPython provides startup file capabilities, described here: http://ipython.readthedocs.io/en/stable/development/config.html . Typically you would put these here:
~/.ipython/profile_default/startup/ . When testing, don't be alarmed that any print statements in your startup files don't show. This is also true in a lone qtconsole.
For Canopy, as another (less environmentally invasive but less convenient) alternative, you can start Canopy from terminal and it will inherit the shell's environment (e.g. from .bash_profile).