There might be a slight defference between these two. 她不是在吃东西： The emphasis is that she is doing something else. 她没有在吃东西： The emphasis is on denial. She is not eating.

1 means that she does not "eat" something. Maybe she's drinking or doing something else. 2&3 are the same meaning. 沒=沒有。 she isn't eating something.

Thanks Yuan!

All of them should be correct and same meaning. It is means" she is not eating.". 不是 is like "not" in English, which is a very common response to the negative scentence. 没有/没 reprensent " no" in last two sentences. In Chinese, all these type are ok. But last two is more native.