LogFAQs > #979328755

Aragami is a neat, though obviously low budget, stealth game where you can teleport between shadows. There's a more refined sequel, but I haven't played it.

Shadow Tactics is one of the very rare Real Time Tactical Stealth titles, though you are controlling between 2-5 people at any given time, and technically, one of them is just a very stealthy samurai.

Mark of the Ninja is probably considered old by now, but by visuals and controls I'd still consider it modern. Of all ninja games I've played, this one probably puts the most emphasis on being stealthy.