In the dialog for entering the data for a 1099-R, after entering the data amounts there is a series of questions about the payment and the plan.
On the screen titled "Was This Distribution From a Qualified Plan" you check one of the two boxes to answer it.
Note that the list of types of plans that are 'non-qualified' it does not include any mention of annuities. That is probably because not all annuities are 'non-;qualified'.
If your annuity is fixed and you have no way of taking a loan from it, or otherwise cashing it in, etc., I would think it is probably 'non-qualified'. If you are not sure, you may have to contact the plan.
