You can use MySQL Workbench and other apps if you establish SSH tunneling with your Nitrous box. Run the following command in your Unix console, replacing the variables with the actual values found on your boxes page:
ssh -N -p <box_port> action@<box_host> -L <local_port>/localhost/<remote_port>
From there you can open up MySQL Workbench and connect to host 127.0.0.1 on port 3306. You will also need to ensure your MySQL database on Nitrous is running. Run parts start mysql
to start up the database.
Take a look at the Nitrous.IO guide for a complete walkthrough.