GW, credit heist, raids, GA, TW, TB, various events like Assault Battles are all sources of credits. As you level and gear more characters more options open up.
Mod farming is actually a halfway decent source of credits too. 50 crystals gets you 7.5 T3 mod challenge attempts. Each attempt gets you 7,500 credits and a mod. Sell grey mods (except speed arrows for up to 9,500 credits each (5-dot) and either pocket the cash or use it to level up other mods. Potential 119k credits / refresh and more chances to get promising mods to level.