Missiles are hard to come by as the majority of such ammunition is found by killing enemies that utilize the missile launcher. These enemies are limited to super mutants, higher-leveled Talon Company mercs, raiders, and some wastelanders. Even though these are common enemies, few members of such groups carry a missile launcher at low levels (level 2-14).
Sometimes, the player can randomly find missiles on enemies that do not use a missile launcher.
A player can find more missiles in ammunition containers with the ScroungerPerk. Combined with high Luck, there have been cases of players finding over 30 missiles in one container.
Traveling to the extreme south-east corner of the map, near Rivet City, you can find 2 ammunition boxes exclusively containing missiles on the wreckage of a ship. You will have to swim across the river to get here.
Over 28 split across three ammunition boxes on a wrecked barge just west of Arefu along the shallow river bank. It is guarded by a few protectrons. (Confirmed with Scrounger only).
In an ammunition box next to a missile launcher around the back of the Washington Monument.