Table Wizard is also capable of managing tables which are in a different database from your default Drupal installation. The external database needs to be defined in settings.php:

$db_url['default'] = 'mysqli://root:pass1@localhost/drupaldb';
$db_url['extdb'] =   'mysqli://root:pass1@localhost/otherdb';

$db_url['default'] defines your Drupal database (i.e., this is what you are most likely already assigning to $db_url). 'example' represents another connection, and the text you use in place of 'example' will appear in the Table Wizard pages to qualify tables as coming from the external database.

Once you do this, the Available tables list on the Table Wizard page will also show tables in the external database, in a separate select list. At this time, although Table Wizard does not prevent you from creating relationships across databases, the Views module does not support this.