The location for mysql.sock on my system is /usr/local/mysql5/mysqld.sock
thrilllap-2:tmp reuven$ mysqld --print-defaults mysqld would have
You'll have to dig up the exact syntax, but for MySQL I think they use a unix_socket query opt. Something like:
unix_socket
mysql:///dbname?unix_socket=/opt/mysql/mysql.sock'
Should be your connect URI for SQLAlchemy.