My daughter was constantly congested and the humidifier & allergy medication (zyrtec, singulair, claritin) never really worked--until she was diagnosed with a milk allergy. As soon as all milk was cut from her diet, her congestion disappeared. You could try to cut out cows milk/diary from their diet for just a month and see if they improve.
When her congestion was really bad, we gave her a salt water sinus rinse (in each nostile). Had to promise/bribe her with candy rewards because she hated it so much, but it definitely cleared out her nasal passages. Neil Med makes a pediatric sinus rinse kit and has pre-measured pediatric salt packets. You can ask your pharmacy if they carry the Neil Med kits. Our local grocery store pharmacy carries it.
(Of course, you don't mention if their congestion tends to plague them with secondary ailments: sinus infections, post nasal drip coughing & eventual bronchitis, pink eye, ear infections... You might want to consider a food allergy if they have secondary ailments in addition to runny noses)