Sudafed should probably do the trick - how long is your flight? You may need to take a second dose during the flight. You should keep equalizing your ears by yawning during ascent/descent. Also you should be able to find saline solution nose sprays at the chemist/drug store - this will have a calming effect on the mucous membranes.
If you can speak to your ENT doctor before flying that would certainly be a good idea.
For the long term google neti pot. This is something used historically by yogis to rinse nose and sinus/eustachian tube. You put lukewarm salt water in it and pour through one nostril letting it come out the other. This similarly has a calming effect on the mucous membranes.Pretty much doing what Loose Rivets suggests without the mess :-)