IGs have full authority to conduct criminal investigations (as well as audits and evaluations). I'm pretty sure it would be rare for the FBI to get involved just to help -- if it's joining an investigation, it presumably sees potential federal crimes worthy of its attention. One possible factor is that FBI has jurisdiction over all federal crimes, not just ones that touch the Transportation Department (though I wouldn't venture to guess where that line gets drawn).
Of course, none of this means there will ultimately be a prosecution, or if there is, that it will have anything to do with the cause of the crashes. For example, if it turned out that one of the FAA employees involved held Airbus stock, that would likely be a federal crime.