You can use Sequel Pro with Vagrant by setting up SSH under ‘SSH’ on the connections page.
The MySQL credentials will be the ones used inside of the Guest VM.
For example; Host, Port etc won’t be the same on your host machine, so use the host and port number that MySQL recognizes inside of the VM.
For your SSH, use the Host that you specified in your Vagrantfile, and the SSH user unless changed should be ‘vagrant’. Then for the password (unless changed in your Vagrantfile) you are going to need to click on the key icon in the password field. This will open a dialog to open a file, so then find the private key that vagrant created and select that.
Usually the private key can be found at ~/.vagrant.d/insecure_private_key