I want to know best way for uploading binary to itunestore. Is it through Application loader or using Xcode organizer archive build, validate and submit.
You don't use Application Loader in Xcode 4 anymore. You can only upload through the Xcode Organiser...
As zekel mentions below, you can still use Application Loader to submit your IPA files. The Xcode Organiser method is useful if you are building the app yourself and want to validate and submit from one place. Application Loader method is useful if you have the IPA signed to the correct certificates installed on your system.
After using both methods, Application Loader gives you more indication of progress status which is useful if you are on a slow connection.