Two of the three men spotted popping out of a manhole onto an Upper East Side street near the hotel where Israeli Prime Minister Benjamin Netanyahu stayed during his appearance at the United Nations General Assembly have been arrested, police said Friday.

The suspects — Kevin Rodriguez, 26, and Samuel Reveron, 25 — sparked an underground security sweep by the NYPD Wednesday because the manhole, at Park Ave. and E. 61st St., is across the street from the hotel where Netanyahu usually stays.

Netanyahu, who spoke at the U.N. Thursday, had not yet arrived in the city when the black-clad suspects were seen on video about 4:35 a.m. Wednesday, climbing out of the manhole, then escaping north in two vehicles.

Police believe the trespassers went underground a short time earlier through a subway access gate at E. 63rd St. and Fifth Ave.

Cops tracked down and arrested the two suspects on Thursday.

The underground trespassing is the latest in a string of similar incidents, including a May 28 intrusion through a Brooklyn manhole that led to two arrests.

Police said Wednesday’s underground trio, like others in several similar incidents, are not terrorists but more likely urban explorers or migrants searching the sewer system for valuables.

“We have seen a number of incidents over the past few months of individuals going into the sewer system to look for valuables and other scrap metal after a storm,” the NYPD said in a statement.

Rodriguez, of Flushing, and Reveron, of Elmhurst, were charged with trespass and conspiracy.

Their arraignment in Manhattan criminal court was pending Friday.