If your male is intact, neutering him may help.
If you do not plan to neuter him (or if he is already neutered), unfortunately there is not a sure way to stop the whining. A bitch in heat is very stressful for a male dog to smell and not be able to get to her, whence the whining.
One thing to try is to keep them as far apart as possible.
Another option is to find someone to doggy sit your male or take him to a kennel during the worst part of your bitch's heat cycle.
Also, they sell (or at least used to sell) chlorophyll tablets that can be given to a bitch in heat to supposedly reduce the odor. Maybe even giving your bitch a bath may help a bit.
Or you could try to make it harder for you male to smell her - try putting a tiny amount of vicks vapor rub under his nose (don't overdo it because it's strong smelling stuff).
An option for you is to get some earplugs.
Hope this helps!