You forgot Montano Cartel, Black Hand Branch in San Esperito, Japanese Hired Ninjas, Japanese WWII Ancient Soldiers, Gambler's Den Gambling Group, Black Hand Branch in Medici, eDEN Corporation, Black Hand Branch in eDEN Objects Network (Airship, Lacrima and Stingray), LNP, Gearheads, Los Artistas, Los Demonios and Darkwater xD

But, actually, I think The Agency and all Black Hand branches are the strongest organizations in Just Cause universe. San Esperito Military, Panau Military and Medici Military are just common soldiers with practically equal training and equal weapons (and transport). However, Medici Military is the strongest one because of Bavarium power. And Black Hand exist since 1512 (which makes it the oldest organization in JC universe), they are technologically advanced, they do have weather control technology, their weapons are State of Art, they use mechs, they use drones, they use tanks, jets, and everything and everywhere. But... The Agency is US faction and we all know who takes the first place in military activites in our real world. Since they are American, they have gear even better than Black Hand (but their weapons are worse). The grappling hooks are awesome, they use parachutes, wingsuits (JCM) and hoverboards. So... this is a hard choice.

BUT I CHOOSE WWII JAPANESE 100 YEAR OLD SOLDIERS ON HANTU ISLAND! HELL YEAH!!!