You typically need to use glibtool and glibtoolize, since libtool already exists on OS X as a binary tool for creating Mach-O dynamic libraries. So, that’s how MacPorts installs it, using a program name transform, though the port itself is still named ‘libtool’.
Some autogen.sh scripts (or their equivalent) will honor the LIBTOOL / LIBTOOLIZE environment variables. I have a line in my own autogen.sh scripts:
case `uname` in Darwin*) glibtoolize --copy ;;
*) libtoolize --copy ;; esac
You may or may not want the --copy flag.
Note: If you’ve installed the autotools using MacPorts, a correctly written configure.ac with Makefile.am files should only require autoreconf -fvi. It should call glibtoolize, etc., as expected. Otherwise, some packages will distribute an autogen.sh or similar script.