As the title states, those with a jb4 tune in the NY area how have you gone about doing so? Unplug the connector from the jb4 that connects to the obd2 prior to inspection? Would this cause any issues? Any help is appreciated, thanks. Car does not have donwpipes.

As long as you are not throwing any check engine lights you should be good.

Hopefully you have the BT module, just for general ease of use, but anyway. What I did for Maryland state emissions (self service kiosk with an OBDII plugin) is this:

Put car in accessory position:
Open JB4 app
Set to MAP 0
Turn off car
remove OBDII connector
let car sit for 5 minutes with key far away
Start car normally, drive to testing facility

Passed without issue.

Not sure if you have a visual inspection or not, with some good wire routing you could probably even sneak an installed JB4 though that since there's so much plastic in the engine bay. Otherwise, probably safer to uninstall completely for any kind of invasive visual inspection.