The real answer, I suppose, is that with creativity, any class can be a good assassin. Even a Paladin, under the right circumstances.
My personal choice:
LG/LN/LE Soulknife/PsiWar or Psion/Kensai
CG/CE/CN Soulknife/PsiWar or Psion/(Pyro/Cryo/Electro/Sono/Aceto)Kineticist.
Can wear armor or do without, passes every security check for weapons, spell foci, material components or spellbooks, can't be disarmed, versatile self-buffs, and his weapon simply gets better and better...
Potential to do ability damage (depending on build) to spellcasting stats makes him dangerous to any class.
The chaotic version can approach under flag of truce and kill mere instants later.
Expanded Knowledge gives him access to powers that help his offense, defense or even escaping ability.
Decision between PsiWar or Psion is based on personality- is the guy a big bad combatant w/lots of feats or a flexible killer?
When I play PCs like this, I always think of:
Blue Oyster Cult
Shadow Warrior
(Eric Bloom - Donald Roeser - Eric Van Lustbader)
I have no home. I live within my mind.
I have no one. No one I'm bringing up to the sky with me.
No weapon - I carry no sword, only my hands to protect me.
No laws - I obey no laws; my spirit is righteous and free...<snip>