In today's version it is not possible to model the ownership of the database you are deploying towards. The ownership is determined based on the person who creates the initial database, SQL Server inherits the information from the security context of the session that invokes CREATE DATABASE.
So if you execute CREATE DATABASE from a sessions under the security context of a Windows authenticated user, say MyDomain\MyUser, the database is owned by this user; if you execute the command under the context of the standard SQL Server security context of 'sa' the database will be owned by 'sa'.
There is no way to set the ownership as part of the CREATE or ALTER DATABASE statement, which is why it was not modeled in the Database project (.dbproj) properties.
If you want to enforce certain ownership you can achieve this by adding a post deployment script which calls sp_changedbowner. These are the step you have to follow.
If you want to see this modeled in the project, please add your comments to https://connect.microsoft.com/VisualStudio/feedback/ViewFeedback.aspx?FeedbackID=286032