We are always asked whether we recommend using the www. or non-www. of a domain to attempt to rank with, especially in webmaster tools. The answer depends on several factors.
First of all, if you are not sure which structure you should use on your existing website there is a great tool that will make that decision for you based upon which version of your website has a stronger SEO standing. SEOmoz created this tool that will tell you whether the www or the non-www should be your preferred domain based upon various factors.
After you make an educated decision about which domain to use, you can tell Google what your preferred domain is by logging into your webmaster tools account and going to site configuration -> settings (see image below).
Please note, now that you have chosen your preferred domain, it’s important that you have both the www and the non-www in your webmaster tools for several reasons. First of all, technically both the www and the non-www are different pages according to Google so in order to be able to choose the preferred domain you have to verify that you “own” both the www and the non-www (see image below).
Most importantly, if you have conflicting data in the www and the non-www you are going to experience similar issues to Google not knowing what your preferred domain is. In addition, if someone has access to your webmaster tools accounts, say the www, and you only have access to the non-www and make changes you are not going to move the needle because of this conflicting information, especially if you are trying to change things like the crawl rates, geographic location, etc.
Finally, always make sure you webmaster your webmaster tools account. NOBODY should have access to your webmaster tools account unless you love/trust that person. Access to your webmaster tools account is like giving someone your alarm code so make sure you know who has access at all times to protect yourself.