It should be easy enough to tell: if the ii is a mere lengthening for effect, the negative of kowai would be kowakunai with a possible lengthening to kowakunaii for the same effect. If, however, kowaii is intrinsically an alternative form, it should have a negative kowaikunai in addition to kowakunai.
(Modulo my forgetting Japanese grammar, which is quite possible. In any case, there would be some grammatical effects if there was a word consisting of stem + suffix kowai-i.)
Either seem to be common, though one of the Urban Dictionary entries had a point - the extra 'i' adds a third syllable, where "kowai" only has two syllables. I've heard both spoken, maybe "kowaii" is more of a cutesy way of saying it?