I think both are informal ways of saying "What are you doing (now)?"
What's the different between the る version and the るの version?
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Firstly, it should be noted that ending a sentence with の like that is generally more feminine.
In more depth, の (when it is not a particle) can be viewed as a proxy for another word. In a sentence like this, I think it's generally to safe to say that it's something like 訳. Outside of that, in "何をしているの" the の tends to soften the speaker's tone (hence why it is generally feminine). In this case, the の is generally supplying a tone of seeking/giving explanation, which you'll see written in beginner-level Japanese textbooks.
In a similar, more masculine sentence, 今、何してるんだ, the の (here, shortened to ん) does not perform that softening role and is overshadowed by the だ which makes the sentence more forceful. However, the "explanation" intonation is still present.