Both could be correct, it just depends on what you mean. "Is your family in Bolivia?" Would just be asking if someone's family is currently in Bolivia.
Example:
Robin: "Where are you from?"
Ulrich: "Bolivia."
Robin: "Really? Is your family in Bolivia right now?"
Ulrich: "Yes."
"Is your family's in Bolivia?" Would be asking if something of your family's is in Bolivia.
Example:
Jeremiah: "Where is your family's house?"
Kyo: "Japan, yours?"
Jeremiah: "My family's is in Bolivia."