I think the 1060 3GB is worth the extra $30. Like I said, Rise of the Tomb Raider is the only game I know of where we can see a real performance hit in benchmarks because of the 3GB of VRAM. The 1060 3GB will give you GTX 980 level performance in most games while the 470 is usually a little below a GTX 970.
The 3GB of VRAM could become more of a problem in more games in the future but tweaking the settings a little bit should get you back up to 60 FPS while still having good visuals. If you click this link and then scroll down past the videos to the performance chart you will see what I'm talking about.
http://www.eurogamer.net/articles/digitalfoundry-2016-nvidia-geforce-gtx-1060-3gb-vs-6gb-review
In Rise of the Tomb Raider if you turn the textures down from "very high" to "high" the framerate on a 1060 3GB jumps up to 74 FPS and is only 1 FPS behind the 6GB 1060 and the game will still look great. The "very high" texture setting is what causes the game to be a VRAM hog. The rest of the settings can be left on very high.
The point is that the 3GB 1060 might require some settings tweaks on games in the future because of it's VRAM but I think the 470 will need tweaks more often because it is less powerful.