Yakushima is a place to splash out on if you can. The quality of accommodation is world-class and below are just a selection of the more exclusive places to stay on Yakushima. All speak English and you can book direct or email if you have any questions - just follow the links.

An exclusive resort set away on the mountainside with a large pool overlooking the forest. Top class villas are dotted around the resort with electric carts to transport you around. 
We stayed here and explain more: Sankara

Part of the JR hotel chain, it sits on the clifftop in Onoaida with stunning sea and mountain views. It has its own onsen and restaurant.
For the exact location see Google maps

A giant hotel just south of Onoaida set in its own grounds. It has a tree growing in the lobby, its own onsen and a shuttle bus connecting to the airport/port. Being part of the Iwasaki chain, it offers a range of packages.
For the exact location see Google maps

Conveniently placed across the road from the airport with its own extensive onsen (with 5 different baths). You can stay in small round cottages or in the main building.
For the exact location see Google maps

For more information about Yakushima accommodation check out the one and only Yakumonkey Guide to Yakushima