You can use Highcharts or any other libraries with lightning.
First you need to upload your libraries (highcharts & jquery) as static resources to your org. To do that you go to Setup | Develop | Static Resources. You can learn more about it on Salesforce Documentation .
It might work with CDN too as http://code.highcharts.com/highcharts.js, but you might have problems with dependencies.
Once you have your libraries uploaded they will be available to you under /resources
. You can then load then to your component and/or app using <ltng:require />
.
<ltng:require scripts="/resource/jquery, /resource/highcharts, afterScriptsLoaded="{!c.AMethodOntheComponentController}" />