With an afternoon arrival, you could just go straight to Kyoto - It adds 2.5 hours to your journey, but I guess you want to (a) see Tokyo or (b) get some rest?

For the journey to Kyoto, you can start at Tokyo Station (as previous posters suggest), Shinagawa Station, or Shin Yokohama Station. So a hotel within striking distance of one of those stations is ideal. Your choice depends on how price conscious you are and whether you're interested in seeing Tokyo or just planning to relax.