Ame-onna is a female spirit illustrated in Toriyama Sekien's Konjaku Hyakki Shūi as a woman standing in the rain and licking her hand. She is described as a goddess from China's Mount Wushan, who is a cloud in the morning and rain in the evening. She may be considered a rain-bringer for crops.

Why this spirit is considered a youkai and not a kami? As far as I know, this youkai is beneficial especially to farmers. What are the characteristics that distinguish a youkai from a kami?

Well, looking at the kanji literally, a youkai is a strange being (more specficially - suspicious), and a kami is a god (or divine in nature). It's common in lots of different areas of Japanese culture for things to overlap each other, and this is possibly one of the areas - there's probably no definite definition or distinction between the two that would satisfy your question.
So, what one being is could differ from one author to another. In this case, it's a foreign god, so that might be why it's under youkai - in this case, meaning a being that isn't known very well or doesn't reside in Japan. But there's a big but here...

Did it actually say it was a youkai though? Kami are often found in "youkai" books. In my 'youkai encyclopaedia' (and it's called that), there are about ten kami out of the hundred beings in the book.

The term youkai, spirit and goddess are used interchangeably to describe this being that adds to my confusion. I think the case is similar to the kappa. Some people consider the kappa as a water deity.

From what I've read of ame-onna (Japanese texts), it normally says that it's closer to a rain god than a youkai. And the original page for ame-onna in the Hyakki Shuui doesn't actually state that it's a youkai, and mentions that it's a goddess of the mountains. Like I said before, you often find kami among youkai in these sort of books. The only information on the original page is pretty much what you provided.
Perhaps your confusion has more to do with differences in translation. That's probably the biggest thing that confuses people - and why I always try to get the original text and read it myself.

Maybe you're right. I also prefer to use certain terms in their original language because it really creates confusion to the readers.