These words have different connotations, and together represent the whole of the magic lore.
The word ['witch'][1] (and the male equivalent,  warlock)
has clearly negative undertones and is associated with dealings with dark powers and curses, while the word ['wizard'][2] meaning sage, wise man has a much more positive meaning.

It is also intriquing that the word 'wizard' is a relatively late one (circa the XVth Century AC), which likely means that the original name of the Hogwarts school (which was founded at the end of the Xth century AC) might have been a bit different, or (unlikely) that the cultural exchange between the magic and the muggle community was extremely slow.

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 classic example is the brewing of various love potions (amorentia for example).
It's intriguing that even through in the 1990s the knowledge or skills required for brewing the potions is not restricted to gender, the Weasley twins marketing efforts are still mainly focused on the witches, clearly they are the target audience as it is apparent from 
the labeling of the product and their sales speech :
 

> “Haven’t you girls found our special **WonderWitch** products yet?”
> asked Fred. “Follow me, ladies…” "..." Near the window was an array of
> violently pink products around which a cluster of excited girls was
> giggling enthusiastically.   "..." “There you go,” said Fred proudly.
> “Best range of love potions you’ll find anywhere.” Ginny raised an
> eyebrow skeptically. “Do they work?” she asked. “Certainly they work,
> for up to twenty-four hours at a time depending on the weight of the
> boy in question…” “…and the attractiveness of the girl,” said George.
Draco's Detour - HBP

Tradition, I guess. There is also a wide range of cleaning and cooking spells used by our resident housewife,  Mrs. Weasley. It may be that originally spells and potions like those also were considered 'witchcraft', being less sophisticated than the more 'wise' spells of Wizardry.

Other than these examples, the distinctions, which once were probably more prominent, so much so that they required the creation and usage of two different words,  'witch' vs 'wizard' are almost nonexistent now in a more or less egalitarian magic community, and the words 'wizardry' and 'witchcraft' have the same meaning, (though unsurprisingly when referring to mixed gender groups the accepted term in our patriarchal language system is 'wizards' and not 'witches'.)

All this is pure speculation of course, it's equally possible that Rowling just liked the fancy name or that it is about gender equality as @Gallifreyan suggests and the question @Valorum linked provides a sufficient answer and there is no difference between the two words, and we're once again overanalysing uncompicated matters...


   
  [1]: http://www.etymonline.com/index.php?term=witch
  [2]: http://www.etymonline.com/index.php?term=wizard