Both McAlister and Flynn played in the New Zealand Maori's 19-13 victory over the Lions on June 11.
"Luke is a midfield back who also covers 10 and can kick goals," said All Blacks coach Graham Henry.
"He has been in good form with the Junior All Blacks, who beat Australia 'A' on Friday night."
Witcombe strained a medial collateral ligament and will undergo further medical assessment this week.
"We have to wait for a definitive word on Derren's availability, and Corey's presence is insurance for the squad in case Derren's knee is no good," said Henry.
Mauger was ruled out of the remaining match in the Lions series on Sunday after suffering a hamstring strain in Saturday's match.
Man of the match, fly-half Dan Carter, will also miss the third Test at Auckland's Eden Park because of a shoulder injury.
The All Blacks coaches are also waiting to see if Carl Hayman recovers from an infected toe that ruled him out of the second Test.
Henry will name his team on Wednesday.