It's sort of the same thing as when Sisko gets promoted to captain in "The Adversary" and O'Brien comments that he is the best captain in Starfleet. Was O'Brien, who had served aboard the Enterprise, meaning to slight Captain Picard? Were the writers? I don't think so. It's just a nice thing to say, and less awkward than "Here's to one of the best captains in Starfleet, a distinction which also belongs equally to Captain Picard."
After way too much Star Trek and about the right amount of beer over a weekend, my friend and I had a giggle fit thinking about this scene, because he also said the same thing about Benjamin Maxwell of the Phoenix. So we came up with this bit of drunken dialogue to rationalize it.
"Captain Sisko is the finest captain I've ever served under."
"Hey, Chief, what about Captain Picard?"
"Oh, right. The finest STARSHIP COMMANDER I've ever served under, and Captain Sisko is the best space-station-with-a-starship-assigned-to-it-captain I've ever known."
"Oh. OK, Chief. Where does Ben Maxwell come in?"
"Sigh. OK. Ben Maxwell is the finest starship captain who retired after having a nervous breakdown. Picard is the finest captain still commanding a starship. Sisko is the finest captain of a Bajoran space station. Are we clear?"
Go drink 14 beers and then read it. Believe me, it gets better.