In Kill Arie, Part 1, Gibbs leaves the building to get a coffee. DeNozo and Abbie are in the lab working. Arie shoots through the lab window trying to kill Abbie as Gibbs walks by. They send cops to Anacostia park across the river which is where Arie is shooting from. The shot is fired at 12m30s into the episode on my copy.

Look at a google earth view of NCIS headquarters. The park is across the river from the front of the building, where the ship is docked. You see this when looking out of the office window. The Lab is in the basement on the left side of the building with a sidewalk close to the building. You see this as Gibbs walks by the window.

Arie couldn't have shot through the window because that side of the building is parallel to the direction of the shot as opposed to 90 degrees to the direction. The lab side faces a narrow street and a set of buildings. Not the river side. Yet at 13m15s Arie looks through his scope at the window, dead nuts 90 degrees to the window. At 13m20s Aries' truck drives away from the site. The view clearly shows the capitol dome and the ship moored in front of the building. The truck is parked way off to the side near the 11th st bridge, and the lab side of the building wouldn't even be visible let along facing the shooter.