I use one gallon of white vinegar in a bucket of water to clean all pumps. I like to soak my powerheads and submersible pumps for a few hours. Allowing them to run during their 'soak' works even better.
If the pumps are really encrusted/dirty, then soak them overnight if possible. Having a spare pump to use while you soak them comes in handy.
I usually make a large batch of vinegar water (1 gal vinegar + 2-3 gal water) every 6 months or so to clean all the pumps and powerheads.