This gives a fairly good summary: http://boards.na.leagueoflegends.com/en/c/player-behavior-moderation/5dmkJinG-3rd-party-applicationsmodifications-whats-allowed-and-what-isnt
This is a more official source: http://boards.na.leagueoflegends.com/en/f/cIfEodbz/d/5kx4F7VE
Both feature this part, which Riot does not seem to have revoked so far:
{quoted}
For now, custom models and artwork sit firmly in a "use-at-your-own-risk" category, but we're keeping an eye on them. We can't optimize for assets we don't develop, and if they do become a concern in the future (ie. they provide measurable player advantage), we'll take action based on the stance we just discussed.
Keep in mind that this is talking specifically about the custom skins themselves. Programs that provide custom skins can still be forbidden, if they also provide other features, regardless of whether or not you use those features.
I believe(!!!) Wooxy is fine, but it's probably a good idea to search around the forums to be more certain.