Luigi Mangione, 26, appeared in court on Monday to be arraigned on 11 state criminal counts, including murder as an act of terrorism.
As well as the state-level charges, he is also accused of federal (national-level) stalking and murder offences that could lead to a death penalty sentence.
Prosecutors allege that Mr Mangione shot Mr Thompson in central Manhattan before going on the run. Authorities later arrested him at a McDonald's in Pennsylvania.