Are you staying at the same location for 5 days?

I would definitly contact the hotel/ryokan to examine the possibility to check in early. It's a pain to having to go there from the airport to just drop of your bags and not be able to change/shower. You might ge able to work something out.

If it was me I would split my stay in 2 locations, 5 days in one place would be too much for me in this big a city. But it all depends on what you plan on and like doing... You will be travelling by subway anyway so a day trip by train could work as well. Plenty of options, and it's nice to travel to some of the smaller places for a day.