Well I don't know about Kerala ..but yes no doubt shilling is the most beautiful place to visit . There are many place to visit there .you can go to local sight seeing in shillong then the major tourist attractions are sacred forest, dawki( enjoy boating in the crystal clear water), cleaniest village in Asia also you can visit to cherranpunji from there .
Depends on what you expect out of the trip.both are beautiful places.If you like mountains and cool climate and don't mind hiking to places then visit Shillong.If you like beaches and a typical tropical climate complete with coconuts and pristine sands visit Kerela. Happy Travelling :)
I will suggest shillong as its the best time to see that place and you can be away from this super hot westher and kerela is really humid .
you can go to many places if you choose shillong because all the other seven sister cities are very close to each other .