I would vote librarian, as he has several decent setups. The chaplain is really optimized for leading an assault unit. However, I think the commander is the most flexible. Here's my simplified rundown:
Librarian: tooled-out, probably the strongest individual IC
Chaplain: cheaper, best leader for a squad, specifically assault
Commander: especially for the master, best unit for the whole army, because of his conferred Ld
It depends where you want him to go too. A chaplain is a natural for the assault squad. A cheap master is great on the back line with his troops. And a librarian in terminator armor is a beast deep-striking with term bodyguards. I've also heard good things about both chaplains and librarians on bikes.
Librarian: tooled-out, probably the strongest individual IC
Chaplain: cheaper, best leader for a squad, specifically assault
Commander: especially for the master, best unit for the whole army, because of his conferred Ld
It depends where you want him to go too. A chaplain is a natural for the assault squad. A cheap master is great on the back line with his troops. And a librarian in terminator armor is a beast deep-striking with term bodyguards. I've also heard good things about both chaplains and librarians on bikes.