Make sure you have these settings to be able to connect remotely (i.e. with MySQL Workbench of Sequel Pro) to your MySQL database in a Vagrant VM.

Remote connect to MySQL database in Vagrant VM

Don't run the mysql deamon with --skip-networking option and don't restrict it to
allow connections only from the VM. In order to do that, comment out
    bind-address SOME-IP-ADDRESS
settings in /etc/my.cnf, or bind your host machine's IP address too.

Grant all privileges for the root user in mysql:
    GRANT ALL ON *.* TO root@'%' IDENTIFIED BY 'root';
    GRANT ALL ON *.* TO root@'localhost' IDENTIFIED BY 'root';

Enable port forwarding in /etc/ssh/sshd_config:
    AllowTcpForwarding yes
    
Restart the sshd service and you're done:
    service sshd restart

Now you should be able to connect to the MySQL database in your VM through SSH:
    MySQL host:     127.0.0.1
    Username:       root
    Password:       root

    SSH host:       host-or-ip-of-your-vm
    SSH user:       vagrant
    SSH pass:       vagrant