I can't recollect if I've ever heard a native speaker say, "I'm joking".
The ones I can remember are:
I'm messing with ya
I'm just messing/goofing around
What are the other popular ways to convey the same?
"I'm joking" (or "I'm only joking") is extremely common and probably the most idiomatic way to express this.
There are probably countless ways to say the same thing, most suggestions would be slang and these may be particular to dialects of English (British English, American English etc) or even more remotely to regional dialects.
This is by no means an exhaustive list.