My tip would be to forget about Tokyo (it's a huge city and it's 80 minutes away on the fastest train!) and take one of the frequent Keisei line trains to Narita City instead. It's only a ten-minute ride away, there are plenty of hotels right at the station and they're inexpensive but clean and nice.

Narita is and feels like a small city, and on arrival, you will have time to walk along the Omote-sando shopping street, reach the huge temple area and look around. There are plenty of restaurants on Omote-sando and by the station. Genuinely Japanese.

Makes a nice one-night trip + you can sleep longer the next morning as you'll be close to the airport.