We are arriving in late September at Gatwick at 6:45am from US and are traveling to Paris the same day at 1:00pm on the Chunnel. What is the best way to travel from airport to train station?

You can get a train from LGW to ASHFORD and join Eurostar there.
http://www.londontoolkit.com/travel/...r_transfer.htm

Do you mean Eurostar or Eurotunnel through the Channel Tunnel?

If the former it would be a lot quicker to take the Gatwick Express to Victoria then a taxi to Waterloo.

You should arrive there by 9:30am giving you plenty of time to do a spot of tourism - leave your luggage at the left luggage office (£6 per bag)

I wouldn't recommend going to Ashford as basically you'll end up sitting on a platform for 3 hours

Just to add there are no direct trains to Ashford - you'd have to change trains at Tonbridge

Would that be the left as in the opposite of right at Waterloo or is this an area to "leave" your luggage.

"left luggage" is where one leaves their bags for a fee (no lockers - but a staffed baggage storage)