3. We haven't received a single reply = We've received not a single reply.
In 1 above, that is your only choice.
In 2, you could have used either.
My advice to you would be to use the form in 1 and 3, unless you are sure that the form in 2 is correct. That is, "had not been" will usually be correct, whether or not the other version is possible or not.
Student or Learner