I find the Rogue has more continual ability, whereas the NInja has greater capabilities, especially in stealth combat, (Primarily due to Swift action Vanish), but the Ninja runs on a limited pool system. After their Ki Pool empties, they inherit alot of Non-Unchained Rogue's flaws.
I'd say I prefer Unchained Rogue for the situation you are asking for; if you miss the ability to go Invisible, grabbing Minor Magic (Any), and then Major Magic (Vanish) can give you that, though it's a lot clunkier then the Ninja. On the other hand, all you need is 11 Int, and the ability has it's own pool of uses, caping at 10/day. The At-will Cantrip (Acid splash works), is also a good 'hidden weapon', especially since it can sneak attack if you are unseen...perhaps w/ vanish even.
Otherwise, Rogue has better skill mastery with it's Rogue's Edges, and the talents that support those skills, as well as it being better at debilitating an enemy in a fight.
Hell, a 4th level Unchained Rogue (Thug) can drop an effective -8 penalty on an enemy's attack against them, by rendering them Shaken, Sickened, and Debilitated for attack, in 1 attack, at-will.
(Requires Enforcer feat, a nonlethal weapon, and a sneak attack)
i would say that the ninja can better specialize and the rogue will be more fixable with few options in combat they will be about the same out side of combat.
At this point, the one real advantage of the Ninja is the ability to pick up Vanish and Invisible Blade.
However, otherwise the Unchained Rogue is better. Do remember that taking a single level in either wizard or sorcerer can get you the ability to use lots of wands without UMD (anything on their spell list). Which can enable you to use vanish, invisibility, greater invisibility. Paying for the wands can be expensive, but it's also a great tool.
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Well, obviously you want unarmed combat, or perhaps a dagger.
If you go unarmed then take your unarmed strikes as your finesse weapon. (I believe it counts, as it is considered a light weapon)
Without a dip...you'd need to sink a feat in improved unarmed strike, however I greatly suggest a monk dip, master of mnsy styles would work great, picking up snake styles to represent counter strikes etc.
I'd say keep away from maneuvers, they will require fest investment and that only makes you on par with others, if you want maneuvers I'd suggest going with the steal line with combat swipe. (Take weapons from your oppenents)
Though IMO snake would better be represented with the monk or brawler classes. Put your skill points into stealth/acrobatics