Makefiles are more versatile, they can be used not just for Javascript files, but for anything. I have a django project that uses lib-fann on the backend, and Selenium for data collection. I wish I had put that into a makefile because I can't remember the commands I used to build it, and now I have to take the time to go figure it out.
Makefiles have conventions for not just building, but also running: "make all" to build, "make run" to run, and if you have an unusual project, you can get plain "make" to print out out some documentation explaining what to do. Webpack has webpack-dev-server but then you have to remember that command.
Ultimately a lot of that could be had by a README file, of course, but Makefiles are easier.