Answer in 3 Parts-when your kindle is outside the US:
For the subscription version of new york times-you have to pay the roaming charges whatever they might be. You cannot download the subscription version via USB on to your Kindle.
For the one off edition of the new york times - for which there is a 50c premium you can download via USB on to your kindle
For books purchased in the Kindle store you can download via USB on to your kindle. Therefore avoiding the $1.99 charge.
My advice is to use the software called calibre(don't know which platforms this is available for-certainly available for the Mac) which downloads many newspapers and their headlines for free. Connect your kindle via USB and it downloads them to your kindle. I would google the word calibre and your will find the download site. I think I am right in saying that calibre has a forum on this very site if you are stuck.