Narita airport overnight layover

Will be traveling from US to Manila and will have a 17 hour layover in Japan from Narita airport. My question is: how long will it take for me to get a shore pass. I am not a US citizen and will therefore need a visa. I plan to stay at a Tokoyo Inn. Landing time is 1600. What time should the hotel expect me to check in. The hotel has a free shuttle.
My flight the next day is at 900. What time should I arrive at the airport?
Thanks in advance for the response.

Firstly you do not say what country your passport is from. Check out www.mofa.go.jp and see if your country of citizenship is listed as Visa free. Japan allows about 66 countries to be visa free for tourist visitors, I think most are around 3 months. If it is then you will just need to fill out the ingoing and outgoing documents as handed out by your airline, prior to arrival. If not then I suggest you contact your nearest Japanese Consulate/Embassy as soon as possible and clarify what is needed. This could take time.
You don't say where the Toyoko Inn is, I presume near Narita, so if your arrival documents are in order, it will possibly be 1 hour or so before you are outside the terminal. Sometimes its much quicker, sometimes slower depends on the number of planes landing round the same time.

You mention your plane departs at 9am. You should be at the airport no later than 6 -6.30am, again its all dependant on number of departures at a similar time. Its much better to be early, than panicking about missing the plane.