Shillong market place has plenty of hotels. For Cherapunji, I have stayed in Four Season Eco Resort (8575937759, 7628071725) which has a pretty good location. Dawki has river campsites to stay in.
OYO have very good hotels to offer n Shillong. Choose any one of them.
Visit all the sight seeing places in Shillong . You should also not miss following :
Cherrapunji
Dawki Lake
Mawlynnong village : the cleanest village in Asia
Bangladesh Border
Living root bridge