You can mess around with the SVG code to change the fill color of the tooltip's <path> elements to make it transparent. I don't think you can do transparency with the VML version of the charts, though (use by versions of IE older than 9). Here's example code that does it:
http://jsfiddle.net/asgallant/UK8Jy/ (note that the example uses jQuery for browser detection and document manipulation, but you can use other libraries or plain old regular javascript to accomplish the same thing).