Change libtool used in command line
Unless your $PATH is different than normal, you could solve that with a sym link of the tool you want.

$echo $PATH
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin


Then if the libtool you want to run first is /usr/local/libtool/bin/libtool then a quick

sudo ln -s /usr/local/libtool/bin/libtool /usr/local/bin


At that point, you might have to restart your shell or rehash or hash -r in bash to get the libtool from /usr/local/bin to be preferred.