Guwahati Airport is the closest one to Shillong. There is a also one small airport at Umroi, about 35 km from Shillong as well, it has fewer flight options as opposed to Guwahati Airport.
Guwahati Railway Station is also well connected to almost all parts of country.
Hotels in Shillong
Though we went there without prior booking but i would recommend booking in advance as in peak season, its hard to find a good hotel on the spot. We couldn't find a hotel in Police Bazaar, so we stayed at Blue Pine hotel in GS Road which was well connected with all parts of city and was beautiful inside.