The Thunderbolt port can be used for Mini-DisplayPort. In theory, you should be able to use Target Display Mode because you are using a Windows machine as your primary display. [See Use your iMac as a display with Target Display Mode and How to transmit my PC onto my iMac?. However, as mentioned in the latter link, you can use Microsoft Remote Desktop. Therefore, you could try using a Mini-DisplayPort to Mini-DisplayPort cable, but Microsoft Remote Desktop would be a safer bet.
Instructions for Target Display Mode:
Update: the Late '09 iMac can accept Mini-DisplayPort connections, so you should be able to use a Mini-DisplayPort cable.
- Make sure Make sure both computers are turned on.
- Connect the Mini DisplayPort or Thunderbolt cable between the two computers.
- Press Command-F2 on the keyboard of the iMac that you want to use as a display.
- To exit, press Command-F2 on the keyboard of the iMac that you want to use as a display.
Instructions for Microsoft Remote Desktop:
- Download the Remote Desktop Client from the Mac App Store.
- Set up your remote PC to allow remote connections. (Allow Remote Access in Control Panel)
- Create / Edit Remote Desktops, or add Remote Resources using the Remote Desktop client.
Creating a Remote Desktop
- On the Connection Center screen, click New.
- In the Edit Remote Desktops window, enter information for the remote desktop connection
- Click the close button to save the remote desktop.