It means "Are you having a laugh?" as in "Are you kidding?".
It's rhyming slang. It's usually used by people who have a Cockney accent.
It's all about rhyming, really. Bubble -> bubble bath. "Bath" rhymes with "laugh." So instead of saying "Are you having a laugh?", they drop the "bath" part of "bubble bath" and say "Are you having a bubble?".
A similar example would be "Are you having a Turkish?".
Turkish -> Turkish bath -> laugh.