The main office of the Forsyth Nature Center in Kingston, N.Y., was also ransacked, Kingston police said.
One of the unidentified 16-year-olds was charged with felony burglary and the other with the misdemeanor of criminal trespass, police said, adding more charges were possible.
Both boys were released with court appearance tickets.
The Kingston Daily Freeman did not report if police said what type of bird was killed or if the animals tormented with a water hose and the pig released from its pen were now OK.
The 76-year-old zoological park and garden, originally called the Forsyth Park Zoo, is home to birds -- including a muster of peacocks -- reptiles, pack animals, small mammals and insects. It is also a reserve for rescued domestic or non-releasable wild animals and includes a small botanical garden.
The zoo, managed by a conservation society, was open Friday and had its scheduled pre-Halloween "Boo at the Zoo" educational event for elementary schoolchildren and their families.