Police said 2-month-old Promise Lee and 2-year-old Love Lee were taken near 17th Street in Jericho around 6:45 a.m.
Authorities say it happened following a fight between the mother, 31-year-old Sun Shin, and their father inside their home. The mother was located hours later, and no charges are expected.
Authorities had issued a silver alert for her on Sunday, saying she was suicidal and threatened to take her own life and her children's lives.
It is unclear where they were found.