To clean my hydors and my powerheads I take hot water (as hot as can come out of the tap, mix about 2 gallons of that with 2 gallons of white vinegar and I run them for an hour in the solution. I then remove them and rinse them under boiled distilled water and let them sit in that for an hour. Once they have no smell of vinegar to them I give them a good rinse again just to be safe and put them back in the tank. I also have a similar cleaning regiment with my skimer just that it's pure vinegar at first then it's straight water after that.
FYI sometimes that hydor needs to come apart to be cleaned as well. it can be a PITA to put back together but cleaning those gears inside makes a huge difference too sometimes.