Of the two, "taken aback" is stronger, in my opinion. It's also exclusively a negative reaction, as far as I know. "I was surprised by my friends at the airport" is a positive experience. You couldn't substitute "I was taken aback by my friends at the airport" and have the same positive tone to it. There's a sense of shock and drawing back, either physically or emotionally, as the result of being confronted with something.
"Surprise" can be anything from mild to something of a shock, but I would say that "taken aback" tends to be more akin to shock. It's certainly more graphic and figurative. The root of its meaning is to be slowed down abruptly, and possibly quite violently, by a change in the wind (when sailing). I would say that it is far less likely to be used in everyday conversation than "surprised" or "shocked", however. I agree with James, my own explanation notwithstanding, that the image of someone drawing back is the one that occurs to me on hearing the phrase.