The easiest and recommended answer is to use ember-browserify. (as support for bower packages will be removed in the future.)
This is an example for using the npm package dexie within an Ember CLI app.
Install browserify: npm install ember-browserify --save-dev
Install dexie (or whatever module you need): npm install dexie --save-dev
Import the module like this: import Dexie from 'npm:dexie';
UPDATE (April 2021):
ember-browserify has now been is deprecated in favor of either ember-auto-import or ember-cli-cjs-transform
(see the deprecation warning at the top of ember-browserify)