It doesn't really matter when when your wife applies for the residence card, because the residence card is not mandatory:
You don’t need to apply for a residence card as a family member ...
She probably wants the card anyway, of course, because among other things it will document her right to work and to enter the UK if she travels internationally.
If she is concerned about having a gap between the expiration of the EEA family permit and the receipt of the residence card, then she should apply as soon as possible. On the other hand, if she'd rather delay the expense associated with the application, she can do so. I do not know how long a residence card application is likely to take, but if you can find out, you and your wife will be able to decide for yourselves whether it makes sense to delay the submission of her application.
(The decision on when to apply may also depend on your own status, since you must be able to prove that you are a "qualified person." You've probably already done that, since she has an EEA family permit.)