gtx 1060 variant

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Aside from performance, which will probably be very similar, the two cards each offer a different collection of ports on the back. The Gigabyte card offers 2 DVI, 1 HDMI and 1 DisplayPort, while the MSI card has 1 DVI, 2 HDMI and 2 Displayport. If you use, or plan to use multiple monitors, that could be useful to keep in mind. Also, the MSI card is longer at 275mm compared to 223mm for the Gigabyte (and a bit wider too), which could potentially affect your choice if you have a really small micro-ATX case, for example. The coolers on them are also a bit different, but you might want to check reviews for each one to determine which cooler performs better, or is quieter in operation.
The performance difference is very small between these two cards. There isn't a "better" model out there. All are identical in performance, unless you need that extra +2 FPS more than the other card gives.

Get the one you like the best.
 
Either one of the 1060's you have listed will be fine. As said by ThomasKK, the difference in core/memory clocks doesn't really give one of these cards an advantage over the other.

At this point, it is all about your preference.

I own that exact gigabyte card you linked and am quite happy with it.
 
With GPU boost 3.0 they all pretty much will operate up to whatever temperature and power allows. A little tweaking and you can turn practically any card into the same performance as any stock clocked card.

Out of the box I have a 1080 that boosts to 2012Mhz, I think it is rated at 1836Mhz or something like that.
 
Aside from performance, which will probably be very similar, the two cards each offer a different collection of ports on the back. The Gigabyte card offers 2 DVI, 1 HDMI and 1 DisplayPort, while the MSI card has 1 DVI, 2 HDMI and 2 Displayport. If you use, or plan to use multiple monitors, that could be useful to keep in mind. Also, the MSI card is longer at 275mm compared to 223mm for the Gigabyte (and a bit wider too), which could potentially affect your choice if you have a really small micro-ATX case, for example. The coolers on them are also a bit different, but you might want to check reviews for each one to determine which cooler performs better, or is quieter in operation.
 
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