I'll only name the skills I think would be worthy of slotting from the two (ARCHER and PUGILIST) that seem the most likely. Taking into account that there is supposedly a TP regen skill inherent to Ninja's meaning ...it won't need Lancer.

Archer:

Venemous Bite makes sense with the Ninja using Poisons.
Quelling Strikes suits a Stealth classed designed to avoid enmity.
Raging Strikes for the most powerful Ninjutsu.
Straight Shot for a good crit boost.
Hawks Eye mostly for the ACC boost and if Ninjas do decide to use dex...emphasis on if, then this would be a very nice cross class skill indeed.

Pugilist:

Featherfoot = Evade = Stealth Class!
Second Wind as the oh shit heal.
Internal Release, stacking with Straight Shot will mean the NIN can optimize their gear with Skill Speed probably (and not worry about crit as much!)