I also suffered from clogged ears for a long time (years). It went hand in hand with clogged sinuses. I finally found relief with a two-pronged approach, attacking it from both the inside and outside:
1) hydrogen peroxide in the ears. I would lay on my side and fill up one ear at a time with peroxide, then let it fizz for 15 minutes. I would do this a few times a week.
2) I upped my vitamin C intake to around 10-20g/day. I feel that this was really the major factor that helped me get over it. My theory is that the large amount of vitamin C (ascorbic acid) helped turn the pH of my sinuses/eustachian more acidic, thereby making them inhospitable for fungus.
3) I took a tablespoon of ACV 3-4 times a day. ACV is superb at breaking up phlegm/mucus, and also helps acidify your body where it should be acidic (digestive tract, sinuses, etc.).