You can walk there from Nippori station. Actually most of the way is via pedestrian-only street, so if you don't carry too much luggage, it's worth walking anyway. Otherwise take a taxi (we took one from Tokyo station).
we took the train to nippori station It is about 6 stops out of tokyo station.
Both Nippori Station (if coming from Narita Airport) and Sendagi Metro Station are very close. Go to Annex Katsutaro web site and view their two videos on how to walk from these stations. About a 10min pleasant and safe walk from Nippori Station. About 2 min easy walk from the Metro Station. Have fun!
Get an answer from Annex Katsutaro Ryokan staff and past guests.