These words have different connotations, and together represent the whole of the magic lore.

Although at the time Harry studies at Hogwarts there seems to be no discrimination whatsoever between students based on gender, still it seems that historically there are potions and spells accociated more with witches - the best example is love potions, for example amorentia. There is also a range of cleaning and cooking spells used by our resident housewife,  Mrs. Weasley, and it may be that originally spells like those were considered 'witchcraft'.
The name of the school may suggest that the founders, when they institutionalised the magic education  collecting all the knowledge, (whether it was known as 'wizardy' or 'witchcraft') wanted to make clear to the community that they intend teach all if it.

It's pure speculation of course, it's equally possible that Rowling just liked the fancy name or its about gender equality as @Gallifreyan suggests.