The answer to above concern, for many webmasters is both. The data in Google Analytics is about what happens after a user chooses to visit your site; whereas, Webmaster Tools reports are more focused on data from before the user makes that choice.
Google has now integrated Google Analytics and Webmaster Tools, via a limited pilot, for Search Engine Optimization reports in Google Analytics, based on Search Queries data from Webmaster Tools.
This includes query information, clicks, impressions, clickthrough rate, and average position. You’ll also be able to use Google Analytics advanced data filtering and visualizations with this data.
In addition to including Search Queries data found in Webmaster Tools, these Search Engine Optimization reports also take advantage of Google Analytics’ advanced filtering and visualization capabilities for deeper data analysis. For example, you can filter for queries that had more than 100 clicks and see a chart for how much each of those queries contributed to your overall clicks from top queries.
To enable these Search Engine Optimization reports, you should sign up for the pilot and you must be both a Webmaster Tools verified site owner and a Google Analytics administrator. Each additional user who would like to view them also needs to individually sign up for the pilot.
The sign up sheet for the pilot is closed for now.