Garchomp: Pros: Can Have Very high attack, Good Speed, Very strong Mega Evolution, Mega Garchomp has highest stat total of all 3, can cover weaknesses well. Cons: Mega is very Slow.
Zygarde: Pros: Highest regular stats out of the 3, immune to ground, can run many different types of sets. Cons: Slow, Shallow move base.
Flygon: Pros: Very Fast, Good Coverage, decent attack, plentiful move set, Easily Banded or scarfed. Cons: Lowest Stats out of any of the 3, weaker defenses.
Out of all 3, I would choose Garchomp, but it's your choice.