Algae eaters are not specific fish. They are simply fish that eat algae including plecos and otos.
Now, for the difference. I have owned otos in the past and they are very fun fish to have. They also do a great job on the algae. They do create less waste, but you have to keep a school of them so it probably adds up to the same amount of waste. The problem with them is that they are extremely sensitive fish. The slightest change in water will kill them. Also, they often are malnourished while being prepared to get shipped to fish stores, and sometimes, if they don;t get food, they won't eat when they do get food and then they starve to death.
I personally prefer plecos because, though they grow bigger and are messy, you can keep them by themselves, they come in all different sizes and colors, and they are very good at eating algae. I currently have a clown pleco who managed to clean my tank filled with algae in about three days. What I really like about them though, is that they are very hardy fish which obviously makes them easier to care for. They also have really fun personalities, but otos do too.
I guess, in the end it depends on your skill level, how much work you are willing to do, the size of your tank, and your tastes.