These days Google revealed they are working on secure search, the SSL search, using https:// protocol.
If you are signed in your Google account and make a search query in Google.com, your query won’t be accessed at Webmaster tools of people’s sites you are visiting.
But if you are signed out, your query will be viewed. Anyway if you are paying Google you will be able to view the referral information.
Alternative ways for collecting data are still Bing and Yahoo tools.