Lagares was injured while beating out a double-play ball Monday night in New York's 7-3 win over Arizona.
An outstanding defender, Lagares had performed well in an everyday role after Chris Young went down with a strained quadriceps at the beginning of the season. Lagares was leading the Mets with a .314 batting average and a nine-game hitting streak.
Young is eligible to come off the disabled list Friday.
Nieuwenhuis hit .310 with two homers and eight RBIs in 10 games with the 51s.
Right fielder Curtis Granderson also was out of the lineup Tuesday night after injuring his left forearm and ribs when he collided with the outfield wall Monday. He is day to day.