Think also about airport transportation. IMO the most convenient is the Friendly airport limobus door to door to your hotel, from/to both HND and NRT, but you need to check the schedules carefully as some hotels have very frequent service while other (sometimes larger) hotels don't.

Yes you can take NEX to Tokyo station (or.....) and transfer to the subway system (or a taxi), but this is bad with luggage as you typically must walk up and down stairs and the transfer path in major stations can be a long walk.

It's common for people, including locals, to take the limobus to/from a convenient nearby hotel with good service but again you're probably then transferring to a taxi. Moreover, for the return to the airport, hotel guests have priority, so you could face a problem with being left behind if the bus you need is full.