Is it safe to take niacin and milk thistle together?

Yes. Milk thistle has very few interactions.

On the other hand, the mechanism of niacin's beneficial actions aren't well understood, but they seem to involve how it is processed in the liver. So if I were taking milk thistle and niacin, I would be inclined to take them a few hours apart, so that the liver can deal with the niacin without the milk thistle interfering...