Well, you can certainly get the IIS "root" folder from the registry.
It can be found in the following location:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\InetStp\PathWWWRoot\
and some very simple VB.NET code to retrieve this value could be something as simple as:
Imports Microsoft.Win32
Module Module1
Sub Main()
Dim rootFolder As String = Registry.GetValue("HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\InetStp\", "PathWWWRoot", "").ToString()
Console.WriteLine("IIS Root Folder: " & rootFolder)
Console.ReadLine()
End Sub
End Module
(The above code sample is run from a console application and contains no error checking etc.)