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Одним из решений является использование UI Automation . Поэтому вам нужно добавить ссылку на UIAutomationClient и UIAutomationTypes, а затем использовать код, подобный следующему примеру:

// get the foreground window handle.
// here I used the Windows GetForegroundWindow function but you can use
// any function that defines what is the active/foreground window in your context
var foreground = GetForegroundWindow();

// get all Visual Studio main windows (from the desktop)
foreach (AutomationElement child in AutomationElement.RootElement.FindAll(
    TreeScope.Children, new PropertyCondition(AutomationElement.AutomationIdProperty, "VisualStudioMainWindow")))
{
    // note the unfortunate 32-bit that UI automation uses instead of IntPtr...
    // in practise that shouldn't be a problem
    if (child.Current.NativeWindowHandle == foreground.ToInt32())
    {
        // this is the foreground Visual Studio
        // get its DTE instance
        var obj = GetVisualStudioInstance(child.Current.ProcessId);        
    }
}

// see doc at https://docs.microsoft.com/en-us/previous-versions/ms228755(v=vs.140)
public static object GetVisualStudioInstance(int processId)
{
    CreateBindCtx(0, out var ctx);
    if (ctx == null)
        return null;

    ctx.GetRunningObjectTable(out var table);
    table.EnumRunning(out var enumerator);
    var monikers = new IMoniker[1];
    while (enumerator.Next(1, monikers, IntPtr.Zero) == 0)
    {
        monikers[0].GetDisplayName(ctx, null, out var name);
        if (Regex.Match(name, @"!VisualStudio.DTE\.[0-9]*\.[0-9]*:" + processId).Success)
        {
            table.GetObject(monikers[0], out var obj);
            return obj;
        }
    }
    return null;
}


[DllImport("user32")]
private static extern IntPtr GetForegroundWindow();

[DllImport("ole32")]
private static extern int CreateBindCtx(int reserved, out IBindCtx ppbc); // from System.Runtime.InteropServices.ComTypes