Mac OS X 10.10 mySQL 5.6.26 accessible from CLI but not port 3306
I had this same problem too, and changing the port in /Library/LaunchDaemons/com.oracle.oss.mysql.mysqld.plist fixed the issue, with no side effects so far.

Changing the port in my.cnf didn't work. It makes the Preference Pane say that MySQL is not running, and makes it impossible to start from the Preference Pane.