The big forward is headed to New York from Portland in exchange for a draft pick and allocation money.
The move isn't a shocking one as the Timbers were disappointed in Cooper's play during the 2011 season.
The former FC Dallas forward has been inconsistent at best since leaving Major League Soccer for Germany in the summer of 2009 and will now be headed to his fourth team since joining 1860 Munich from Dallas.
Cooper's four goals in the final seven games of last season made arguably raised his trade value to the point that New York felt willing to take a chance on him. The move could also foretell one of New York's current forwards being on his way out of the club in the near future.