Depending on arrival time, another option would be to just skip the Tokyo stay and go straight on to Kyoto. Flights from the west coast of the US tend to arrive in late afternoon. It would be pretty simple to just jump on the Narita Express to Shinagawa and immediately change to the Nozomi (bullet train) to Kyoto, arriving by 8 or 9 pm.

If your friend really wants to stop off in Tokyo for the night, I'd agree the two easiest choices are Tokyo and Shinagawa. If he wants to get out and see some of Tokyo, then Tokyo Station would be better. If he just wants to crash for the night, choose Shinagawa.

Low- to moderate priced hotels can be found on:

www.japanhotel.net or
http://travel.rakuten.com/

Major chains like Hilton, etc can be booked on their sites. I don't think there is a Hilton close to either Tokyo or Shinagawa.

Any of the Prince Hotels near Shinagawa Station would work pretty well. Aside from the one shown on Japan Hotel Net, others can be found at:

https://www.google.com/webhp?source=...+station+tokyo

Actually, if your friend is only going to Kyoto, the easier way would be to skip Tokyo and fly directly into Kansai Airport (KIX). From there it is only a 75 minute direct train to Kyoto Station.