Not necessarily "makeconfig", but the actual file "Makefile". "Menuconfig" is simply one of the options that is supported by the Makefile. Just like "make" and "make modules_install". Menuconfig and modules_install are called targets. The targets that are supported by a program are usually inside the "Makefile" (this is a physical file, by the way). If that file somehow got corrupted, then those targets may no longer be available.
Can you try re-emerging gentoo-sources? What I was referring to when I suggested re-extracting was going to www.kernel.org,
downloading the particular kernel version you wanted (which comes as a .tar.gz or a .tar.bz2 file), and then using 'tar' to extract the sources. I'm using Slackware and this is how I download and extract a new kernel since "emerge" isn't available to me.