Transport to hotel late at night

My boyfriend and I are traveling to Japan this September and our flight into Narita Airport arrives at 8:05PM on a Friday night. Our hotel is in Shinagawa and we're wondering how we are going to get there so late at night.

I've checked the NEX timetable and theres a train at 8:44pm and 9:44pm that travels to Shinagawa Station. Since we'll need to get our baggage, go through customs, activate our rail passes and reserve a seat, I'd say we'd probably miss the 8:44pm train. Therefore catching the train at 9:44pm, we should get into Shinagawa at 10:46pm

My main concern is late check-in in Japan. We're staying in a hotel a couple of minutes away from the station so I'm assuming we'll be fine for it but I'm not sure.

Is this the best option for us? I'm curious to know before I go and book our flights. My biggest worry is missing the train and being stuck at the airport overnight and paying for a hotel I can't sleep in, which we both shall need since we leave Australia early in the morning that day.

My main concern is late check-in in Japan. We're staying in a hotel a couple of minutes away from the station so I'm assuming we'll be fine for it but I'm not sure.

Most hotels have no problems with check in until midnight, especially the larger ones. But you better specify the late check-in time at the time of reservation.

Is this the best option for us?

Yes, I think it is the best option. Another option could be the aiport bus:
http://www.limousinebus.co.jp/en/bus_services/narita/ebisu_shinagawa.h...

My biggest worry is missing the train and being stuck at the airport overnight

Don't worry. It is not going to happen. In the unlikely case that you miss the 21:44 Narita Express, note that there are more trains after than (althoug slower). And in case of a multi-hour delay (extremely unlikely), the airline would take care of you.