As rkkwan points out, Waterloo to Paddington, then the Heathrow Express is probably the best. I recently took a taxi from Paddington to So. Kensington for about 10 GBP, and again from So. Kensington to Waterloo for about 12, IIRC. The Heathrow Express is 13 GBP.
Alternatively, and if funds are not tight, a taxi - or driver - Waterloo-Heathrow might run 40-45 pounds, and sure makes for an easier trip.