I had the same problem, running Mountain Lion with Ryby 2 installed and being used instead of the standard system ruby.
Previously I added PATH=/usr/local/bin:$PATH to my .bash_profile as a way to make sure stuff installed by homebrew, including Ruby 2, take precedence over some system stuff.
Anyway, in this case I was doing
sudo gem install cocoapods
and after a succesful install, when trying a 'pod setup' I would get
-bash: pod: command not found '
so I noticed that cocoapods would install their 'pod' binary not in
/usr/local/bin
but rather in
/usr/local/Cellar/ruby/2.0.0-p247/bin/
So to my .bash_profile I added
PATH=$PATH:/usr/local/Cellar/ruby/2.0.0-p247/bin/
and now cocoapods works like a charm.