Don't forget that there was the novelization of Far Beyond The Stars. While I haven't read the novel (although it is on my shelf and on my "To Read" list), as I recall the episode Sisko and his 1950's counterpart, Benny Russell, were the lead characters.
But with the numbered novels I don't recall any one particular novel centering him out. Sisko did play big roles in the novels, but it was kind of like he was there, but we need to focus on the rest of the ensemble. The Siege had Sisko in it, but it was more an Odo novel, whereas Bloodletter was a Kira novel and both The Big Game and The 34th Rule were novels about Quark. I do recall that in The Long Night, Sisko is presented as being an amateur historian on the long-lost emperor that people are looking to find in that book, but that's a book where all or most of the cast members seemed to get their own scene.
Good question by the OP and this is a good observation by Tom Swift. Sort of reminds me a lot of the TV shows, where Sisko is there, either in the mix or prominently in the background, but the episode is about something or someone else.
I'm wracking my brain trying to think of Sisko-centric stories that I've read that haven't already been mentioned and I can't think of many. Granted I only read a handful of DS9 numbered novels though, but the only one I can think of that was mainly about Sisko was Saratoga. Back then I did find it very similar to Reunion but I didn't mind so much since it gave me a glimpse at Sisko's history. From what I recall, I don't think that MJF's Saratoga characters stood out as much as his Reunion characters did.
I didn't see the Lost Era's Catalyst of Sorrows mentioned. I thought it was a decent entry in that series and I liked the idea of Sisko and Tuvok teaming up.
There is the novelization for Emissary too that you might want to check out. I'm guessing the What You Leave Behind novelization probably has a lot of Sisko in it, though I am guessing here since I didn't read it.
There was the book Hollow Men (I haven't read it), but Sisko is on the cover and I thought it was supposed to be a sequel to "The Pale Moonlight".
As for DRGIII's recent Sisko-heavy trilogy, I've got mixed feelings about it, trending toward the negative. I think Raise the Dawn at least mitigated some of the damage of Rough Beasts and Plagues of Night that DRG did to Sisko's character. Why he felt the need to try to return Sisko to a Season 1 mindset is beyond me. (Outside of Emissary and a few spots here and there Season 1 Sisko was too remote a presence. He got much better as a character after he shaved his head.)