Witcher 3 by a country mile.
Now don't get me wrong, I loved Skyrim. But Witcher 3 has a much stronger narrative to really draw you into the world. Even the side content in Witcher 3 is much more fleshed out and diverse. Sure Skyrim has more freedom and character options, but while the lore and world may be a vast ocean, the central plot and narrative that is supposed to pull you in is a deep as a puddle.
However this could easily go either way. From a gameplay perspective, both have their ups and downs. On one hand Skyrim is much more consistent while on the other Witcher 3 make a much harder effort at telling a story. Something like this will obviously boil down to personal preference.