Okay....I just had it explained to me by a caller to a radio show, and now I can agree that Chase is very, very good.
First of all, the guy who walked and sat at the counter was Phil Leotardo's nephew introduced in some earlier episode. Second, he walked by Tony to go to the bathroom, and as Tony was facing the door, he would be able to get to next to/behind Tony with a gun after he left the restroom. Lastly, remember when Tony and Bobby were in the boat, and Bobby makes that comment about not seeing or hearing it coming. THAT'S what we saw: Tony got shot in the head, and the last thing he saw was Meadow entering the restaurant!
I feel stupid for not realizing it, especially since Chase probably "borrowed" it from an well-known early episode of MASH where Hawkeye's journalist buddy talked about "not hearing the bullet" when you get shot in war, and then he gets shot in the same fashion.