First, if you can remove and machine wash the case of the cushion(s) that were peed on, that is the best way to get them clean. If the cover is removable but not machine washable I would still take it off and wash it by hand.
Then I would clean the cushion itself with bac-out (a product from biokleen that you should be able to find at a natural foods type store). Baking soda, vinegar, and borax are all also good for deodorising. Whatever you use, really soak the pee spot with it.
You may want to wet the pee area and then blot up the liquid as much as possible several times to get more of the pee out before doing the final soaking. And you may have to do several treatments to get all the odor out.