You are presumably talking about the single place that your family, as a whole, has its origins, so it generally takes a singular verb in this context, "comes". But if you are talking about the individual members of the family, then you can use a plural form, e.g."My family all have very different personalities".

This place is where my family COMES from would be correct!

'This place is where my family comes from' is the correct one :)

COMES is correct