I get most of my energy credit from space combat. Fighting intensive foundry missions such as "Battleship Royal Rumble" yields some of that. There's also the Tau Dewa patrols, in which you get to fight several waves of enemy ships solo.
Special Task Force missions are another possible source, but the loot being split between five players doesn't make it quite as lucrative - however, there's a chance for significantly better drops, and you get dillithium on each run too.
There's also the "Tour the Galaxy" event, which supposedly yields a lot of EC. The more sectors you cover within that span of time, the more energy credits you'll see in return. If you've got a fast ship, I hear you can make over one-million energy credits doing that.
Then there's the Pay-to-Win approach. If you choose to purchase Zen, you can use it to purchase lockbox keys and then sell them on the Exchange - each goes for about 1.4 million if you slightly undersell them (people either buy them to open lockboxes, or play the economy and try to sell them at a slightly higher price than they bought them).