Add header to multi server or instance query (powershell)
If you just want to hard-code the header, you can use the Powershell New-Item cmdlet.  I used the -Force parameter to initialize the outfile with the single header row and the rest of your script uses -Append to add the detail information.

New-Item $outfile -value "Header,Header,Header,Header`n" -Force
Get-Content $servers | ForEach-Object {Invoke-SqlCmd -inputfile $queryfile -ServerInstance $_ -Database master | ConvertTo-CSV -NoTypeInformation | Select-Object -Skip 1 | Out-File -Append $outFile}


If you want dynamic columns generated based on the actual query, you can run an initial Get-Content using -First 1 (to only get the first server) and limit the output to the first row only by using -First 1.  Then, follow up with your usual Powershell script.

Get-Content $servers -First 1 | ForEach-Object {Invoke-SqlCmd -inputfile $queryfile -ServerInstance $_ -Database master | ConvertTo-CSV -NoTypeInformation | Select-Object -First 1 | Out-File $outFile -Force}
Get-Content $servers | ForEach-Object {Invoke-SqlCmd -inputfile $queryfile -ServerInstance $_ -Database master | ConvertTo-CSV -NoTypeInformation | Select-Object -Skip 1 | Out-File -Append $outFile}