what do you class as decent hotel? 3 star? 5 star?
i've stayed at shinagawa prince main tower 3 times, love the service, love the location ( 2min walk to JR shinagawa, where all of the shinkansen trains stop at, aswel as the yamanote line). from memory i think it was about $170/night
and for onsen, depends on how far you want to travel, i've been down to 2 places near nagasaki. about a 9hr train ride to one of them, the other is about 11 hr