Hey Ali -
i'm using the same setup you've got. I wish I could tell you what the magic secret was, but i don't know! the thing seems to be largely a mystery.
I installed and activated the shopping cart and the buy now plugins. As I mentioned above, it wasn't working for a bit, but then i realized that i needed to use the nextgen shortcodes themselves instead of inserting from the WP media manager. so long as my NGgallery items have a number in the price field, they show up.
that said, turns out this plugin was more than i needed - so I went with the quickshop plugin instead.
But I'm assuming you were able to activate both plugins... yes? Maybe it's a conflict with another plugin in your setup? Have you tried deactivating everything but ecommerce, buy now, and next gen to see if you can get it working then?