Since you're commuting with potentially a bunch of stuff, I'd stick with the wide three speed which will give you a lot of flexibility.

I would also pick up the front bag for carrying stuff. If you need more space, you might consider something like a Carradice saddlebag. I too would go sans rear rack. But you should add roller blade wheels for the schlepping in Penn Station. It makes a huge difference in my experience.

Have you thought about lighting?