Is it animal cruelty to leave dog alone in cage?

No, only if it is protracted to the point of neglect.

One of the best ways to housebreak a dog depends on confinement when the dog is unsupervised; a properly-sized (just large enough for the dog to lay down, sit, stand, and turn around) crate or cage is the easiest way to do this. If the dog is to be confined for a long period of time, water should be made available, as well as a safe toy to chew on--large enough that the dog cannot choke on it, nor break off pieces to choke on. Generally the dog's collar should be removed if it will not be supervised while in the crate.

A dog that is kept in a crate that lacks proper ventilation, is unsafe, or is left in the crate for very long periods of time without being exercised or provided water may indeed be in a state of neglect, and in those cases it could be considered cruelty. At its best, a crate is a tool to be used in assuring the dog's safety and helping its training, and many well-trained dogs view their crates as a safe spot or refuge to get away from overly active households.

As with so many things, it really depends on the usage. A dog barking in its crate is no indication of whether it is being neglected there or not; many dogs that are perfectly well cared for will bark if left alone even for short periods of time, whether out of separation anxiety, boredom, or the simple fact that more interesting things are happening elsewhere.