Brilliant, brilliant scene, and I think the rocking of the boat on choppy water was completely intended as a means of cranking up the tension. It worked, too. Paulie really is treading on water when Tony starts grilling him. Luckily for Paulie, he doesn't crack.

When I think back to it, it's one of the best individual scenes of the season; look at Tony's inner frustration when Paulie doesn't crack. It's a frustrated gesture (when he considers the knife on the deck but goes instead for the beer) that to me shows how badly Tony takes being "wrong", and how competitive he is within himself - he was treating that conversation as if it were some sort of test for him too, not only Paulie. When he throws the beer at Paulie it was like a child who's been caught in the wrong at school, and knows that the only reaction he can do without losing face is to throw a crayon or something at the wall.

It's always present, of course this needing to restrain passion and keep logic level: look at his tantrum in the Bing in the next episode when he loses a bet and starts throwing chairs at the pool table.