A former top aide to New York Gov. Andrew Cuomo and the president of a state university were among nine people charged by federal prosecutors Thursday in two wide-ranging bribery, bid-rigging and extortion schemes involving some of the governor’s signature economic-development programs.

The sweeping scope of the charges and the details of the allegations contained in the 80-page complaint filed by U.S. Attorney Preet Bharara’s office represent a vigorous censure of the culture of state government that has long been derided...