Personally, I would choose Gatwick; change of trains at Reading. If you fly into Heathrow, you'll be directed to the bus to Reading for the Cardiff train, or you could "double back" into London on Heathrow Express and change at Paddington onto the Cardiff train.
You keep your luggage with you on the train - or rather you can keep it on racks at the end of the carriage, at least on the Reading -> Cardiff.