In the run-up to 2000, I would have picked McCain over Lieberman. Immediately after 9/11, I was thankful that Lieberman wasn't the VP, as I think Gore wouldn't have handled things right, and having someone in office dealing with Muslims who they would view as being under Israel's control would have had deep ongoing repercussions. I didn't have a problem with him being Jewish, but I think it would have caused the US problems.
Today, I've really notched my view of McCain down, and respect Lieberman a lot more than I did. I don't agree with him on everything, but on the whole, I'd take him over McCain.