Absolutely pick something close to the train station, as that is really the only sensible way to do Tokyo. I always like to search for hotels on Google maps that are closest to the stations I will be relying on the most. They make it very easy to search by dates, and the reviews are about as comprehensive and reliable as you will find anywhere. Search for Shinagawa Station and Tokyo station, and click on the Hotels bubble at the top of the map (either option is perfect for your needs). Of course, the map is also ideal for planning how to get around by transit.