Why does my vim command-line path differ from my shell PATH?

This is a known problem introduced by Apple in OS X 10.5 Leopard.

If you are using Bash or Zsh and are using non-interactive shells, you are affected.

Running sudo chmod ugo-x /usr/libexec/path_helper will fix you up, but you should take a look at the article to see why.

From this SO answer

There are many similar questions on stackoverflow and stackexchange.

Your shell executes different *rc files depending on the arguments its given at launch time. Therefore, you need to setup Vim so that it launchs your shell with the right arguments.

The following helps in bash, I'm almost certain there's a similar flag in zsh.

set shell=bash\ -i

See $ man zsh for the right flag and the right execution order.