Which is better
Both.
MEGA has 5V IO and the familiar AVR microcontroller. However, it's pretty much the top AVR available in terms of Flash size, and so has some "egde" failings. Also, it still only runs a 16MHz.
The Due has an ARM microcontroller, and potentially is near the bottom of ARM-based arduino-like boards. It should be much faster than MEGA for many applications. OTOH, it has 3V, relatively low-current IO, and worse compatibility with various 3rd party libraries.
If you need to ask a question like this, I think you would probably be better off not considering either.
Buy a Uno and get a basic understanding of the Arduino environment.
Its like saying which is the best and apple or an orange