Super-, as discussed here, is a prefix that means above, beyond, or to a greater degree. The Latin literally meant above or beyond.
Ultra- is also a prefix, also unchanged from Latin, and also literally means beyond. In English, it can be used to be a synonym of super- or can be talking about physically being beyond something else.
The prefixes are not ranked as one higher than the other because most of the time, a field of study will pick one or the other. Ultrasonic and supersonic are not speaking of the same thing. Ultrasonic is the sound frequency outside human hearing. Supersonic is describing something as moving faster than the speed of sound. There is even a term for power plants that are ultra-supercritical. Basically, when the technology advanced past supercritical the inventors needed another word.
Outside of the United States, most of the time ultra- words are hyphenated. Inside the United States only a few are, like ultra-pasturized. Super- words are not generally hyphenated anywhere. If in doubt, always double-check a dictionary to make sure.
From original creator Tim Kring, the supernatural phenomenon begins again with a fresh crop of inspiring heroes who take on the ultimate struggle between those with extraordinary abilities and those with nefarious motives to hunt and harness their powers. [The New York Times]
The twisting concave building has been likened to be a piece of ultra-modern sculpture, resembling the upturned hull of a ship and contains a lecture theatre and library. [The Oxford Times]