I see that my cowl induction vacuum line goes directly to a vacuum source at the bottom of the front of the carb.

There is also a fitting near the back of the manifold that has the brake booster connected to it, and it has two other un-used connecters that are capped with little rubberized covers.

It seems to be working ok, but would it be better to route it to the fitting instead of the carb? If so, which of the four inlets should it plug into?

The factory routing is to the fitting on the manifold.

However, that should get the same reading as the base of the carb, which is normally used for your PCV valve.