Mega Ampharos is not the best partner for Greninja. Sure, the two are a decent duo, but there is no "best partner" for Greninja. They are both hard walled by specially bulky Fairies and specially bulky Pokemon in general, and can only really hurt certain team styles.
A partner for Greninja that I personally love is Mega Mawile, as the two each do an incredible job at eliminating the other's counters. Mawile dispatches pink blobs and bulky fairies that laugh at Greninja, while Extrasensory Greninja can defeat Mega Venusaur and Gliscor/Hippowdon. The core beats both offensive teams and many defensive teams alike, and in general is pretty solid. Pair it with a Lati@s to provide extra Mega Venu insurance and put pressure on many bulky Waters, and you have yourself a great core that can pressure many teams.
If you are set on using Mega Amphy, however, use Dragon Pulse, Thunderbolt/Focus Blast, and Thunder Wave in the other slots.