I always thought it was miniscule. My miniscule dictionary says:

The standard spelling is minuscule rather than miniscule. The latter form is a very common one (accounting for almost half of citations for the term in the Oxford English Corpus), and has been recorded since the late 19th century. It arose by analogy with other words beginning with mini-, where the meaning is similarly ‘very small.’ It is now so widely used that it can be considered as an acceptable variant, although it should be avoided in formal contexts.