The first time that you click on queries in search engine optimisation you are presented with the following screen:
You have to use the same username for Analytics and Webmaster Tools so that you can link the accounts together and bring through the data from Webmaster Tools into Analytics.
If you are using the same username that you will see the below option appear:
From that you are taken to the “web property settings” where you can confirm that you are the website owner and can share the data. Then you will be able to see loads of interesting search query data.