The Microchip PICkit3 is enumerated as a Human-Interface-Device(HID) in the USB hierarchy.
The MPLABX IDE scans the USB hierarchy to detect all supported device programmers for the controller target specified by the project when the developer starts a debug session or device programming.
You will see the error message: "The project uses platform tool noID but that tool is not installed. From the main menu, select Tools then select Plugins. Install the missing plugin" when no device programming tool has been select for the project.
The list of available device programming tools is populated by all of the device programming tools found when the IDE scans the USB hierarchy.
It appears that the IDE is not finding your PICkit3, so no PICkit3 option is visible in the list of tools that the IDE presents.