How should I terminate a black plastic drain pipe?
You didn't mention if the drain pipe is accessible from under the floor. Assuming it does not pass directly through a concrete slab, the only safe way to terminate and seal the pipe from backwash and septic gas is to cut it off and glue the proper sized cap on with primer and PVC cement.  If and when you need to reinstall the drain, simply cut off the pipe again below the cap and use a coupling to continue the pipe run back to a new closet flange. Do not use a screw cap. They are for temp use or pressure testing only. The hardware can rust, loosen and leak.