1) You can think of Node-webkit as the Chrome browser minus the address bar because in reality, that's what it is. But since it isn't busy doing anything other than running your game it should be faster. In my experience there's quite a bit of performance difference but I have like 20 tabs open in my browser at any time so that doesn't necessarily count for much
2) What kind of laptop? Are the drivers up to date? WebGL seems much more likely than OpenGL to take a performance dive if the drivers aren't fresh.