Are you certain your PATH hasn't been corrupted? I've got the auto-tools in /usr/bin on my machine:
> ls -lah /usr/bin/auto*
-rwxr-xr-x 1 root wheel 13K 16 May 2011 /usr/bin/autoconf
-rwxr-xr-x 1 root wheel 8.2K 16 May 2011 /usr/bin/autoheader
-rwxr-xr-x 1 root wheel 30K 16 May 2011 /usr/bin/autom4te
-rwxr-xr-x 2 root wheel 227K 16 May 2011 /usr/bin/automake
-rwxr-xr-x 2 root wheel 227K 16 May 2011 /usr/bin/automake-1.10
-rwxr-xr-x 1 root wheel 73K 3 Feb 21:55 /usr/bin/automator
-rwxr-xr-x 1 root wheel 20K 16 May 2011 /usr/bin/autoreconf
-rwxr-xr-x 1 root wheel 17K 16 May 2011 /usr/bin/autoscan
-rwxr-xr-x 1 root wheel 33K 16 May 2011 /usr/bin/autoupdate
Edit: it appears I did still have 4.2 on my machine. So this above is probably not helpful in the least.
You could try using the autoconf package from homebrew. It does not appear to be a keg that's available by default with homebrew, but you can still get it from here by placing the following in to /usr/local/Library/Formula/autoconf.rb:
require 'formula'
class Autoconf < Formula
url 'http://ftp.gnu.org/gnu/autoconf/autoconf-2.13.tar.gz'
homepage 'http://www.gnu.org/software/autoconf/'
md5 '9de56d4a161a723228220b0f425dc711'
def install
system "./configure", "--program-suffix=213",
"--prefix=#{prefix}",
"--infodir=#{info}"
system "make install"
end
end