Out of the given options, the naturally occurring species in India are:
Black-necked crane: Yes, it is found in India. It is a winter visitor to the high-altitude wetlands of Ladakh, in Jammu and Kashmir.
Cheetah: No, cheetahs are extinct in India. They were once found in various parts of India, but the last recorded sighting was in 1947.
Flying squirrel: Yes, there are several species of flying squirrels found in India, such as the Indian giant flying squirrel, the Malabar giant flying squirrel, and the red giant flying squirrel.
Snow leopard: Yes, snow leopards are found in India. They are found in the high-altitude regions of the Himalayas, such as Ladakh, Himachal Pradesh, Uttarakhand, and Sikkim.
Therefore, the correct answer is: 1, 3 and 4 only.