You can only make a reservation for the Shinkansen train part of your journey. Note that Shinkansen trains have unreserved seats so you can just turn up and get on a train, although you might have to stand up if it's a busy time of day.
You can reserve seats for the Shinkansen up to 3 days in advance from here on the JR reservation site
You can also reserve Shinkansen seats at any JR ticket office (at all major stations), you can do this any time in advance, or on the day, and even up to ~20 minutes before departure (provided there's room on the train). The time of day you are travelling out of Tokyo will probably be quite busy, so it'd be worth reserving a seat in advance.