Never used NextGen, sorry.
In general the docs in images are short because there isn't much to explain: you put images in some folders, those get thumbnail and published in other folders. Which folder goes where is determined by IMAGE_FOLDERS
Additionally: subfolders work pretty much how you would expect them to.
So, in general, what you need to do is:
1. Get all the images from NextGen downloaded somehow into some folder structure
2. Configure Nikola to publish those folders in the output site
Then if the URLs don't match what they used to be:
3a: change the posts so they use the new URLs
3b: change the image paths so the new URLs match the old URLs better (no idea how NextGen's URLs look like)