I've stayed at the Annex Katsutaro and it's a nice place to sack out. It's also at one end of the Yanaka Ginza; the other end leads to Yanaka cemetery and JR Nippori-eki. That area is part of Shitamachi, the old part of Tokyo which has its own charms, different from the more glam parts of the city.

An option for your luggage if you cannot check in early is to use one of the takkyubin services to have your luggage delivered to the Ryokan. The best way to do this is to address the luggage to yourself care of the Ryokan. Print this out (with the name and address of Annex Katsutaro in Japanese) and tape it to your baggage. Then when you are at the counter, the staff can copy the information onto their tags. Then you can begin your day and arrive at the Annex later in the day.