Well if I were washing algae coated rocks OUT of the tank I'd use a bleach solution to soak them in first as bleach is excellent for that sort of thing and then I would barely have to scrub the rest of the algae off with a sponge. Saves a lot of time and effort, using bleach. I'm a bit paranoid though so I add some extra water conditioner to the tank when I put them back in, just in case there's still bleach residue even though I obviously rinse them very, very well!
If you're not removing them from the tank I don't think there's much choice but to use a sponge/pad/toothbrush and just scrub off any algae you can reach. It's kinda difficult this way, depending on your tank depth and how you have the rocks arranged but if you don't want to mess up the formation of the rocks then it's worth a bit more effort. Plus big rocks are a pain in of themselves to carefully remove from the tank.