The tool can only export what is in the API output. If you are exporting forms you can use the form.meta.username to get the username.
If you want to convert a user_id to a username you can do that with a mapping field. This allows you to map input values like 1234 to an output value like user1. In order to do this of users you will need to export all your users from the CommCare HQ Users page and then put them into your config file for the commcare-export tool with the ID and the username columns.
There is a section on the help docs about this: https://confluence.dimagi.com/display/commcarepublic/Data+Export+Tool%3A+Tips+and+Tricks#DataExportTool:TipsandTricks-Convertoutputvaluesbasedonamapping