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.
My experience is that Npm "kinda works" on Windows. There are mysterious race-conditions and annoying bugs. And I'm not even talking about npm being technically completely incompatible with Windows due to the 256 character path limitation.
There are quite a few packages in npm that require native compilation of some part of their system during install. These usually fail horribly on windows without spending a lot of time tweaking your system in ways you probably don't want to. This is in sad contrast to how well many of the other libraries just work.
I would have thought it'd be possible to emscripten compile something like tinyC, and make a C compiler you could naturally fit into the node ecosystem to build native libraries.
This is almost certainly true, and if there were as many people trying to use node on those operating systems as there are on windows I expect you would see a similar number of complaints.
I also install git bash and conemu to have bash on Windows which makes things much better. I don't use windows console.