UPDATE 2020

The issue suggesting mainDir is now closed. Instead there is a new field called exports which can be used almost like es import maps to map a folder to an export alias:

// ./node_modules/es-module-package/package.json
{
  "exports": {
    "./my/": "./src/js/lib/my/"
  }
}

import thing from 'es-module-package/my/thing.js';
// Loads ./node_modules/es-module-package/src/js/lib/my/thing.js

As suggested in the issue linked in the original answer below it may be possible to map the root to a folder to access import thing from pkg/thing.js as so:

{
  "type": "module",
  "main": "./dist/index.js",
  "exports": {
    "./": "./src/js/lib/my/"
  }
}

Original Answer

For a native solution, see this node issue https://github.com/nodejs/node/issues/14970

The feature request suggests a mainDir field in the package.json next to main.

The more people that vote, the faster/more likely it will be implemented