Currently my website neolisk.com appears as itself and also as sites.google.com/site/neolisk in webmaster tools. Sometimes it is also an issue when users do Google search - results appear under both domains. Is there any way to tell Google Search and Webmaster Tools that both are the same website, and to reference only neolisk.com?
This appears to be an issue for all Google Sites users who have mapped domains to the service - strikingly ironic that Google would not even include the capability to specify canonical links.
Per the Add link rel="canonical" issue report (last updated 7/25/2012):
In the meantime, given that using the URL removal seems to be the only solution, could the documentation for that tool be updated? At the moment it very clearly states that it should only be used in urgent cases and would seem to contradict use as a workaround for this issue.
... so it would appear that your best bet would be to set up Webmaster Tools for both domains and use the URL Removal feature on the google.com content.
One issue with using URL removal on Google Webmaster is that the request per URL removed will expire. And when that happens, the Google Site URLs return on search results immediately. often with higher ranks than the www domain urls. You have to go back and re-request the removals frequently and it will take 2-4 hours for the status to go from "pending" to "removed". This is a very tedious and unacceptable approach - but then it seems like there are no alternatives.