What's this connector used for?
 

I think this is a connector for a vacuum line but don't know what's connected to it. It's on the back of the intake manifold close to the MAP sensor. I know the larger connector has a line that goes to the brake booster.

There is a picture of the stock equivalent just a few posts up. I think that is the vacuum source for HVAC switching but I'm not sure.
https://ls1tech.com/forums/generation-iii-external-engine/881472-broke-sensor-need-help.html

Will this cause a vacuum leak, can it be plugged if I'm using a HVAC?

This is the vacuum connection that operates the HVAC vent doors inside the passenger compartment. If your car is not A/C or heater equipped this can be capped off. Either way, it must have a hose or cap on it or you will have a significant vacuum leak.

Thanks for the help, I'll just cap it now maybe the engine will idle better.

With out this vacuum source hooked up you will not be able to switch the vent settings in your car, it will default to defrost only.