While we'd need more information, such as which Pokemon you're pairing it with, I'll provide my thoughts on each Pokemon.
Gyarados itself prefers more to be a setup sweeper, using Moxie as its pre-Mega ability since it may be able to get off a quick kill before Mega Evolving. Once Mega Evolved, his set prefers to run Dragon Dance / Waterfall / Crunch (or other Dark-type moves) / Filler. For the filler, I suggest using Earthquake for power and to make use of Mold Breaker negating Levitate, or Iron Head to cover Fairy-type.
Sharpedo's main strategy is to Protect once while non-Mega to get a Speed Boost, then Mega and start trying to sweep with Strong Jaw making moves like Poison Fang or Ice Fang very helpful. My personal favorite moveset for him is Crunch / Waterfall or Aqua Jet / Ice Fang / Poison Fang or Poison Jab.
Their main differences lie in which movesets they have and the fact that Gyarados is Water-Flying before it Mega Evolves, which grants a wider variety of resistances. Overall, I'd say go with Mega Gyarados if you want more power Physically, and use Mega Sharpedo if you want to outspeed and cover certain types better.
Let me know of any questions, and knowing the full team would help as well.