This is my ninja build. I can kill a deathclaw or sentrybot with one sneak attack right now. The key to the build is Blitz, Agility 9 perk, that increases the distance you can melee attack in VATS. I sneak close to the target and start VATS, and Blitz lets me teleport to the enemy and sneak attack from relatively far away. With Grim Reapers Sprint I get a chance to refill my Action Points when I kill someone in VATS. Attacking and teleporting uses up a lot of Action Points, but Grim Reaper fully upgraded refills my AP about a third of the time.

Starting Stats

Strength 3

Perception 3

Endurance 2

Charisma 1

Intelligence 5

Agility 8

Luck 6

Ending Stats with bobbleheads and I am Special Book and some perk points

Strength 4

Perception 4

Endurance 3

Charisma 2

Intelligence 6

Agility 10

Luck 8

Important Perks (Max them out unless it says otherwise)

BLITZ is the most important perk so upgrade this first. It allows you to melee attack in VATS from far away and teleport to the enemy. I have teleported through walls before.

GRIM REAPERS SPRINT gives you a chance to refill your AP with each kill. So you can teleport from one enemy to the next, leaving a trail of bloody deathclaws in your wake.

SNEAK