From Hakone to Kyoto - transportation

What is the best way to get from Hakone to Kyoto? And how much does it cost?

Thanks!

After doing the classic Hakone loop course, you can go to Odawara or Mishima by bus for a JR connection to Kyoto.

For train schedule and cost, you can work it out here:
http://www.hyperdia.com/cgi-english/hyperWeb.cgi

It is also explained here:
http://www.japan-guide.com/e/e5206.html?aFROM=2158_5200

I have two pieces of luggage so is the bus between Hakone and Odawara a good idea? If not what's a better alternative? Should I make advance bookings?

Thanks again!

Having your luggage with you while touring Hakone on different means of transport is not a good idea. Use the luggage forwarding service known as Takkyubin to have your luggage forwarded to your hotel in Kyoto the day before. Don't expect the same-day delivery though. You also need to notify your hotel in Kyoto beforehand.

http://www.kuronekoyamato.co.jp/english/services/takkyu.html
http://www.japan-guide.com/e/e2278.html

I recommend to use a delivery service as suggested by William. Possibly send it directly to Tokyo, where I assume you will be staying after Hakone, and bring just a small bag to Hakone.

But if you don't want to do that, I recommend to avoid big luggage on buses. Big luggage on trains is not convenient either, but still better than on buses. So, depending where in Hakone you go, note that you might be able to access it by the Hakone Tozan Railway.