The 18-year-old Ko's astonishing run of making 53 consecutive cuts ended when she shot a three-over 76 in the second round for a two-over-par 148 total, missing the cut by one stroke.
"I just made a double (on the 11th) and just couldn't get anything turned around," said Ko, who had made the turn one-under for the round but bogeyed three of the next four holes after the double.
"I just kind of made bogey after bogey and when you do that, it's not great."
It was a much better day for Kim, 22, who has already won twice in her rookie season on the LPGA circuit.
She shot a five-under 68 on the undulating Westchester course in the leafy northern suburbs of New York City and leapfrogged seven-times major winner Karrie Webb of Australia and twice defending champion Park In-bee.
Kim posted an eight-under 138 total in the second major of the season.
After registering five victories on the LPGA of Korea Tour, Kim has shown her mettle on the LPGA Tour by taking her 2015 wins in playoffs.
"I was inspired by Tiger Woods, how he was able to make shots and shot-making," said Kim. who leads the tour in birdies and eagles. "I was actually able to show all the shots out here on the course today."
Breathing down her neck are two accomplished winners.
The 40-year-old Webb, looking for her first major since 2006, shot 71 in the morning and was joined at seven-under by Park.
South Korean Park surged up the leaderboard late in the day, following her opening 71 with a flawless 68.
Tied for fourth on 140 was Suzann Pettersen of Norway after a bogey-free 66, and 17-year-old Canadian Brooke Henderson (73).
South Korean Jenny Shin, the overnight leader after a 66, reached eight-under three times in the second round but slipped back with four bogeys in her second nine.
Shin shot 75 for 141, a total she shared with world number three Stacy Lewis (71).
The unflappable Kim said she was not worried about going to bed with the lead.
"I believe I can play better in the tournaments where I can feel more pressure," she said.
(Editing by Steve Keating)
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