Going through some meteor libraries, I notice that npm install and meteor npm install are both used in instructions. I know Meteor 1.3
meteor npm will run npm that has been bundled with meteor, this may be a different version than the version of npm installed globally on your system.
You can check versions like meteor npm -v and npm -v
meteor npm install will place the node_modules folder at the root of your project and modify the package.json at the root of your meteor project.
While npm install will work relative to your current directory.
Source: Experience. I'm not 100% certain, but I have used them both a fair amount.