Learn Russian: Кто там? Это птица?

In English, we usually ask "what is it?" when referring to animals. However, in Russian, all animals are considered animate (living beings). Because of this, you must use кто (who) for people, animals, and insects, and only use что (what) for non-living objects.

If I heard a noise and thought it was just the wind, would I still ask Кто там?

No. If you suspect the source of the noise is an inanimate object, like the wind or a falling branch, you would ask Что там? (What is there?). The speaker uses кто in this sentence because they are already guessing the noise comes from a living creature.

Where is the verb "is" in these sentences?

Russian almost always drops the verb "to be" (am, is, are) in the present tense. So, "Who is there?" translates directly as Кто там? (Who there?), and "Is it a bird?" is simply Это птица? (This [is a] bird?).

Since Это птица? uses the exact same words as the statement "This is a bird", how do I make it a question out loud?

You turn a statement into a yes/no question using just your intonation! When speaking, you sharply raise the pitch of your voice on the specific word you are asking about—in this case, птица.