Yes, I think Bill Clinton was lying about Area 51. This was the Jimmy Kimmel show - the only place on earth where a former United States President could talk publicly about Area 51, aliens, and alien visitations without having his sanity questioned. Bill Clinton has always struck me as having a wicked sense of humor. I believe he and Jimmy Kimmel were just on a roll.
I do think Bill Clinton is lying about area 51, but I have no idea what he is lying about. He signed papers that authorize executions if people cross over the borders onto the base, so there is obviously something important there. Then again, it is a military base and these rules usually apply.
Bill Clinton was the president of the United States. He has a level of credibility that is unprecedented. Furthermore, his family is still in mainstream American politics and he is still an active political figure head. Comments that he makes should be taken very seriously. If Bill Clinton made comments about area 51 there is almost certainly a degree of truth in them.
I think that while Area 51 is always going to be popular because of common culture I think the reality is that it's nothing more then a military testing base and it has nothing to do with aliens, I think Bill Clinton is telling the truth when he says that nothing like that happens there.