Landing at Haneda at 9pm - is the monorail still running into central Tokyo, or should I just plan on a taxi?

You're fine - the Tokyo Monorail runs until around midnight, so a 9pm landing leaves plenty of buffer even with immigration queues. Grab a Welcome Suica at the airport or just tap your phone with a mobile Suica. A taxi into central Tokyo runs roughly 6,000-9,000 yen, so save that for if your flight lands late or you're hauling lots of luggage.