Both sentences are possible, grammatically correct, though I would made two minor changes, I would change the preposition and remove "por favor" in the end.
¿Qué quiere comer al desayuno? (formal)
¿Qué quieres comer al desayuno? (informal)
You can also say
¿Qué quiere desayunar? (formal)
¿Qué quieres desayunar? (informal)
If you want to use the preposition "para", then you can say:
¿Qué quiere para el desayuno? (formal)
¿Qué quieres para el desayuno? (informal)
All those sentences are in present, You can also use conditional tense:
¿Qué quisiera desayunar? (what would you like to breakfast?) (It is unusual to use this word as a verb in English, but it is also possible).
¿Qué quisieras desayunar? (informal)
I hope this helps you.