How to find out which terminal app (iTerm or Terminal) is running from within bash
There is an environment variable set by iTerm and by Terminal as the following:

for Terminal:

TERM_PROGRAM=Apple_Terminal


for iTerm:

TERM_PROGRAM=iTerm.app


You should see this variable by typing in env from the command line.

So - using this variable, you can put a condition in your .bash_profile file to select the proper coloring.