Nexus Mod Manager
The NMM is compatible with Fallout 4, and as the years pass and the mods stack up, it'll be pretty much indispensable. What's more, it works with a bunch of other games like Bethesda's RPG, The Witcher 3, Dark Souls 1 and 2, and World of Tanks. It makes downloading and managing mods from the Nexus a breeze.
Fallout 4 Script Extender
As the modding scene for Fallout 4 grows, more and more will use the Fallout 4 Script Extender. It's a utility that allows mods to work without actually modifying the game's executable files, so even if something goes wrong with a mod it won't cause any permanent damage.
With the arrival of official modding tools came Bethesda's own repository for Fallout 4 mods. You'll need an account (it's free) and once you have one you'll be able to browse and download mods even while you're in the game.