"Lucario" is the official Romanization of the Japanese name, "ルカリオ". Whenever you see his name spelt in the Latin alphabet on Japanese sites/merchandise, it's always Lucario. (eg.
http://panasonic.co.jp/center/tokyo/image/050708_img01.jpg)
"Rukario" is a direct, mechanical romanization of the katakana, which, I suppose, Joe used for a lack of anything better. (Better safe than sorry; goofing the Romanization can result in many silly outcomes!) It's simply because he was especially quick with his news (and that he's the owner of these forums, the most popular) that that name spread so well. Direct, mechanical romanization leads to a lot of awkward interpretations of the Japanese names, ie. Kecleon becomes Kakureon. Where an official Romanization of the Japanese name exists (ie. Beedrill = "Spear", not "Supiaa"), I prefer to use it, so Lucario it is!
Another point: When the US developers decide to leave a Japanese name be, as is the case with most legends, they usually use the official Romanization, so there's a pretty high chance (I'll say 90%) that Lucario will be his US name.