Memory Alpha's article on "Far Beyond the Stars" assumes that Sisko's "Benny Russell" experience in that story is a vision from the Prophets. While not citing writer or producer commentary, it does reference lines of dialogue within the Benny Russell vision as corroboration, such as
Then, as he's almost home, Russell hears a preacher (Joseph) on a
street corner who seems to be speaking directly to Benny. "Write those
words, Brother Benny!" the preacher advises – write the words of the
"God of the spirits of the prophets."
MA similarly assumes, and the story itself certainly does seem to bear it out without ever explicitly saying so, that Sisko's vision in "Shadows and Symbols" comes instead from the Pah-wraiths, who have a clear interest in distracting or preventing Sisko from completing what he's trying to do. The problem here is that Sisko never describes his vision to anyone in the story. He just behaves oddly until he breaks through and releases the Prophet who was once also Sarah Sisko.
Various interviews after the series wrapped up note that the writers toyed with the idea of ending the series on a pull-out to Benny Russell, sitting on a set, about to watch his stories adapted into a television series, thus suggesting that the entire series was actually his fictional creation in the first place--that Benny Russell was always real and Sisko always not--but that they decided that, in order for that to work, they would have had to have introduced Benny Russell much earlier in the series.