eu faço isso no IIS 8
$testpool = get-item iis:\apppools\$iisAppPoolName;
$testpool.processModel.userName = $un;
$testpool.processModel.password = $pw;
$testpool.processModel.identityType = 3;
$testpool | Set-Item
$testpool.Stop();
$testpool.Start();
Funciona para mim:)