Reference vega 56 isn't a great comparison. Reference Vega 56 isn't great.
Aftermarket Vega 56 with some undervolting is a different story and is (from what I've seen) slightly faster than the 2060.
Gamers Nexus has an OC'ed 56 in their benchmarks if you want a look. I'm sure they're elsewhere, too.
If you need something now and dont want to tweak, the 2060 is a better option.
If you dont mind a little tweaking and the Vega 56 available isn't a reference cooler, IMO the 56 is the better bet (but they're close).
If you can wait, see what Navi is going to be like. Or at least wait until AMDs CES announcements are all in. There's rumors of Vega 2 on 7nm as well.