Before add-ons required for AF1, a new 747-8 costs 350 million dollars as of August, 2016.
Trump was quoting numbers for the "program" and the program includes two aircraft, not one. The add-ons are determined by the government and most have nothing to do with Boeing. Also, the program goes beyond delivery of the aircraft and includes various updates and improvements for a twelve year period. Some perspective has to be applied to how much cost is for aircraft and how much cost is for airborne command facility.