McAlister of North Harbour is to replace Aaron Mauger, who pulled a hamstring in Saturday's second Test, while Flynn is a precautionary inclusion as Derren Witcombe recovers from a knee strain.
New Zealand coach Graham Henry names his side for Saturday's third and final Test against the Lions in Auckland on Wednesday.
"Luke is a midfield back who also covers 10 and can kick goals," said former Wales and Lions coach Henry. "He has been in good form with the Junior All Blacks who beat Australia 'A' on Friday night."
Meanwhile, England and Lions fly-half Jonny Wilkinson is holding onto an outside chance of making the third Test.
The Newcastle Falcon injured his neck and shoulder during Saturday's outing in Wellington, but said in his column in the Times newspaper: ""As much as it is bad to say that I am used to these (injuries), it is also true that I am used to recovering from them.
"That is why I haven't ruled anything out. I'll take it day by day and go by the physio's advice."