You need to identify the tables for each of the columns that have the same name. You should also be using an IN statement and not = for the department.
I can’t test this since I don’t have your DB but you can try this:
$sql = $wpdb->get_results("SELECT * FROM " . $wpdb->prefix .
"dir_personnel as personnel where lname like '$search%' or fname like '$search%' or
extension like '$search%' or personnel.department IN (SELECT id FROM " . $wpdb->prefix .
"dir_departments as departments where departments.department like '$search%') order by lname");
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