The Fat Man has much greater blast radius of 30 yards with severely reduced damage of 100 before perks.
The Nuka Nuke Launcher has more damage at 150 before perks, and even greater range of 40 yards.
Each MIRV projectile has 100 damage and a 15 yard blast radius.
All will knock down NPCs
In general the Fat Man will be effective at long range shooting at large groups, as an opening salvo.
The Missile Launcher has 300 damage, but a blast radius of 1 yard.
The Missile Launcher has had the 3 and 4 barrel mods removed, as they make no logical sense and the weapon is actually viable now without it.
It will be very effective against single large targets like Behemoths and Deathclaws.
Missiles, Nuka-Nukes and Mini Nukes are now 4 lbs in survival so the weight doesn’t completely preclude their use in Survival mode.
Requires Nuka-World
