The men, 21 and 33 years old, were arrested together with two other men on Wednesday within the laws of terrorism legislation.
The two are also charged with, among other things, rioting, throwing petrol bombs and arson during the riots when McKee was killed.
A third man is charged with, among other things, rioting while the fourth detainee has been released.
29-year-old McKee was shot in the head during riots in Derry in April 2019. The group New IRA - one of the few who oppose the so-called Good Friday Agreement from 1998 - has taken the blame for the fatal shooting and apologized.
The group has claimed that the shooter aimed at a police officer but happened to hit McKee.
A 52-year-old man has previously been accused of involvement in the fatal shooting.
The 1998 Good Friday Agreement put an end to decades of bloody unrest between loyal Londoners and pro-Ireland Republicans.