Perl on Windows is currently built using either dmake.exe or nmake.exe. There is no way to currently build Perl on Windows using a GNU make. Also, ExtUtils::MakeMaker likely does not really support outputting GNU makefiles on Windows.
Traditionally, Perl uses the same toolchain that it was built with for building its modules. I'm not sure why you would want to change that, because that toolchain is proven to work well. Most likely, changing the make utility involves patching ExtUtils::MakeMaker to properly recognize the new type of make tool and produce the appropriate output.