In short: It is not possible, and as it seems won't ever be supported (see here https://github.com/npm/npm/issues/775).
There are some hacky work-arrounds with using the CLI or ENV-Variables (see the current selected answer), .npmrc-Config-Files or npm link
- what they all have in common: They are never just project-specific, but always some kind of global
Solutions.
For me, none of those solutions are really clean because contributors to your project always need to create some special configuration or have some special knowledge - they can't just npm install
and it works.
So: Either you will have to put your package.json in the same directory where you want your node_modules installed, or live with the fact that they will always be in the root-dir of your project.