The first one ("why are you late") is the only correct one, and it is natural, although you may want to use something a bit less direct, depending on the circumstances. The last one would be grammatically correct if we changed the verb to "arrive" or if we said "get here", instead of simply "get" ("get" doesn't mean "to arrive" unless you mention the destination). Number two doesn't work at all; this is because "late" cannot be used as a verb.

Thank you! But 1 is a present sentence isn’t it? Someone late for some meeting ↓ Everyone don’t ask why he is late ↓ After meeting, someone ask he “Why are you late?”? I thought I should say “Why did you late?” Is late adjective?😂 If so, how about ‘Why were you late?’

"Why are you late?" is the correct answer!

Hi! I'm a native English speaker. #1 is natural :)