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Ninja and Slayer are both fairly good at this. Keep in mind that your d3 unarmed strike doesn't have to be higher if you can get enough bonuses added on top. You probably want to TWF, because it maximizes your sneak attack potential, and you can get Brawling armor to mitigate the penalty to attack rolls.
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Is it this Shadow Assassin? I don't know much about this book, but I'll do my best.
Unarmed Strikes count as light weapons, so get Piranha Strike for some extra damage that way. You should also technically qualify for the Daggermaster and Swarm of Blades talents, since you have two fists, even though your GM may not see it that way. (Remember, you have two fists and are therefore "wielding" two light weapons, even if you aren't TWFing. You only take TWF penalties if you try and attack with both fists and get extra off-hand attacks; if you only attack as many times as your BAB allows, you don't take penalties.)
Speaking of TWF, I recommend avoiding that route-- it only pays off if you've got some hefty static bonuses to damage on all attack rolls. Weapon Focus (Unarmed Strike) will help more of your punches connect, which means more damage. You'll also want an AoMF at some point of course, unless you're willing to wear a spiked gauntlet or cestus and call that an unarmed strike. (Though I'm guessing the idea is that you kill secretly, and thus don't want to have anything on your person that can be identified as a weapon.)
I would also suggest you get the Accelerated Drinker trait, and carry a few potions of a suitable buff spell. Magic Fang will boost U.S. damage, Enlarge Person gives bigger damage dice and a STR bonus, Bull's Strength is just straight up more strength. If you have enough skill points to keep UMD maxed out, wands are cheaper per charge, so you could instead get a trait that makes UMD a class skill.
If you can find a practical way to grab them, the pummeling style feats seem like the best option.
This is because it solves one of the primary problems of non-monk unarmed builds- Getting through DR vs. buying an expensive and highly enhanced amulet.
Pummeling style is designed to steal Damage Reduction's lunch money. It pools all of your attacks into 1 attack, which means that DR only applies once. So even if you are facing DR 20, it will only feel like DR 3 when you have 6 attacks.
Because you can pretty much ignore DR, you do not need an amulet of mighty fists that can punch through DR. Thus, you can look towards using greater magic fang to boost your attack and damage instead of buying the amulet (this is usually not a good idea since that spell doesn't do anything to DR)
My advice would be to grab a ranger instead of a slayer based off of this. Since they have spells, and they get greater magic fang on their spell list, then they can do this the need to have very specific team mates. Also, they get TWF bonus feats, which is also nice. The ton of skills also lets them fulfill the role of sneak and scout (even if the flavor is not quite as good as the slayer for this).
Well chosen favored enemies and good use of the instant enemies spell would allow fairly decent damage, and getting the fake pounce of pummeling charge on top of that is just perfect.