Possibly, depending on the motorcycle.
My Suzuki DR200 used about 3 litres/100km, rather less than my Prius hybrid at about 5. My Nissan Leaf supposedly uses 2.1l/100km equivalent, whatever that means. So for a single rider, the motorcycle uses less fuel than the hybrid. Pack the hybrid with passengers, though, and it wins over a bike with 2 up.
That’s just the simple tailpipe emissions, though. There is much more material required to build a car, and there’s an environmental cost to extract that. Cars tend to last longer than small motorcycles, but not enough to compensate.
Cars require more infrastructure than motorcycles - they need wider, stronger roads, and larger parking structures, which are more environmentally damaging to construct and maintain. Granted that I don’t know of any actual built motorcycle roads, but they could perfectly well use a bicycle path. Off-road, motorcycles have less impact and do less damage than four-wheeled vehicles like Jeeps, simply because they’re smaller and lighter.
You can of course get an electric motorcycle, and win both ways.