Try using the contentMouseX, contentMouseY properties of the textArea instance.
No, that's not going to work. The textbox has a vertical scroll bar.
contentMouseY will take the scrollbar position into account. From the docs:
contentMouseY - Returns the y position of the mouse, in the content coordinate system. Content coordinates specify a pixel position relative to the upper left corner of the component's content, and include all of the component's content area, including any regions that are currently clipped and must be accessed by scrolling the component.
If you need the scrollbar position then you can get it from the verticalScrollBar property on the textArea scroller (flex 4):