Any chance at separating the two species? Or getting a larger tank?
Algae eaters are mostly nocturnal, whereas goldfish are far more active during the day. Drop the algae wafers in right before you turn the lights out, and the algae eater should be able to eat in peace. If you are really worried, you can drop a couple in different places around the tank to make sure he finds them. Even place one in a cave where the goldfish can't easily get to it, especially if you want to give him something to snack on during the day. Just make sure to remove any leftovers daily, preferably morning and night, to avoid fouling the water. Placing the algae wafers in only a half at a time will help reduce waste.
I have noticed that my algae eaters (Chinese Algae Eaters) are extremely social with one another. Getting a few more to create a group of about 5, or more if space allows, will help curb aggression issues when they get older, and they will also help each other find food by following each other around while foraging. I am only mentioning aggression issues because Chinese Algae Eaters, specifically, are known to get nasty with other fish as they grow. And they can grow a lot. Having a few more around will help them keep the scrapping within their own group.
Any idea what species of Algae Eater you have? Or, if not, do you have photos?
If you do have a Chinese Algae Eater, it may be wise to bring him back to the store. I love them, but they can cause problems, and they need a lot of space to themselves as they mature. There's really no need for an Algae Eater of any kind in a Goldfish tank, anyway. As you can see, they do most of the eating themselves. Algae wafers are appreciated by them, too, so you don't have to worry about wasting the food that you bought