What kind of problems are you having with it? I'm using npm on Windows and it's working out great! I'm actually using it as my build/task runner rather than using bloated grunt or gulp. It's easy to configure and read. I run my linter, unit test, jscs, and bundler all configured in package.json.

I also install git bash and conemu to have bash on Windows which makes things much better. I don't use windows console.