Given that you and your wife are in the 60s, I would probably avoid the 12:40 AM red eye option, plus that flight is actually operated by American instead of Japan Airlines

The ANA 4:50 pm departure arrives in Tokyo at 9 PM, which is quite late. By the time you get out of the airport and check in to your hotel it will probably by 10:30 - 11 PM. (Although some people may actually prefer that)

Singapore Airlines is nice, but the services on JL are on par with SQ, and when the JL option is $1200 cheaper, I would just take JL.

So now you have to decide to take JL to HND or NRT...HND is technically closer to the city, but it depends on where your hotel actually is. For example if your hotel is on the E / NE part of the Yamanote line (Tokyo, Ueno etc), transit from NRT is actually slightly more convenient than HND. But if your hotel is near the S / SE part of Yamanote line (Shinagawa, Shimbashi, etc), then HND will be a more convenient option

But one more factor to consider given your age - are you and your wife comfortable walking up and down platforms and long distances, with luggage? You can get a taxi from HND to hotels in the city for around 5000 - 10000 yen, while a taxi / car service from NRT will easily be over 20000 yen

So if you sum up all the points above, JL to HND will be my choice