The ATF is a branch of Federal Law Enforcement that operates under the Department of the Treasury, whereas the FBI operates under the Department of Justice. They have exactly the same nationwide law enforcement authority as duly sworn federal agencies. The ATF lately has generally done the "biker gang" investigations of late because they have more experience in that particular field, (see William Queen's yawnfest "Under and Alone") as well as often find large numbers of what they claim to be stolen firearms during such investigations.
Federal Law Enforcement is used in cases such as these because many of the more serious alleged charges fall under Federal Law, known as United States Code or the USC. This would include the racketeering, kidnapping, and witness tampering charges. However, you are correct in asserting that the local "cops" would handle the theft and other more minor charges.