Those are two very different tools. One prevents notes played on a guitar from decaying, while the other loops a tiny fragment of sound.
A Fernandes Sustainer system electromagnetically excites the strings of a guitar, causing them to vibrate for as long as the system is activated. It is the same basic principle as the EBow, but built into the guitar so that all strings can be sustained, and so that the picking hand can be free to do other things. One can still use finger or tremolo bar vibrato, and can slide between notes (neither of which the Freeze can do). The guitar can be played more-or-less normally, save that held notes will not decay.
The EHX Freeze simply loops a very tiny fragment of sound. That sound could be a single note or chord played on guitar, or a symphony orchestra played off of a Sony Walkman. Whatever is “frozen” will sustain for as long as the pedal is on, and you cannot change the sound in any way unless you freeze a new sound. If you want something closer to what the Sustainer can do, the EHX Superego has the ability to slide between the frozen sounds and to modify those sounds via an effects loop. However, it has a far synthier tone.
Both have their uses, and could even be used together. It only depends on what you’re trying to achieve.