Van Gaal sent on goalkeeper Tim Krul for Jasper Cillessen in the final seconds of extra time, and the Newcastle United stopper made two saves in the penalty shootout to send his side into the semi-finals.
Former Netherlands international De Boer believes that Van Gaal's decision shows that he is a special manager.
"It was a genius move," De Boer told talkSPORT. "Van Gaal is the best coach I ever worked with. He is the best chance for a team to have success.
"Nobody really believed in this [Netherlands] team, but I said, 'if one man can change this team, it is Louis van Gaal'. It is the same for Manchester United. Sometimes you need a bit of luck, of course, like we have had in this tournament and it will be the same at Manchester United.
"In the long term you will have success with him, but do you have the patience? He could win the Premier League title, or maybe the Champions League, but it is not really realistic, of course."
Van Gaal will take charge of United after the World Cup.