This is a bit of a pain in the ass because you need to progress through the main quest line AND fully level up the RC Gun to be able to tag special vehicles. There’s also a black one available on a rooftop belonging to STAG later on, but Heli Homie is your easiest method. This one is black, and you can save it to your garage by simply flying it back to your base. You just unlock the Helicopter Homie, who delivers a Tornado helicopter to you. The first way is technically the easiest. The Tornado spawns about here, on the PR Center in SR3 and on a random nearby building in SR4

In Saints Row 3, there are three main ways.

And if your life is getting difficult, the Tornado will solve all your problems. The Condor and Interceptor VTOLs are medicore, no one cares about them. The Tornado is also way stronger than the Void, the alien space craft that you can steal or claim for free by climbing up the massive random towers scattered around digital Steelport. It also seems tougher and more agile than the Vulture, and seems all-round more durable than the VTOL, which I swear explodes if you sneeze on it. In comparison to the other combat helicopter, the Vulture, its barrage of homing missiles are more accurate and easier to make use of compared to the Vulture’s weaker minigun and charge-to-fire streak of missiles. The minigun heats up over time, but the homing missiles are infinite. It has a minigun and an infinite number of homing missiles that you can rain down on your victims with ease.

Saint row 3 guns