Greetings, shaynee:
Well, this is interesting... Personally, I'd go for the Lenovo for these reasons:
a) More RAM (crazy as it sounds, 8 GBs is the bare minimum if you want to do standard productivity and play interesting games these days.)
b) 1 larger SSD (fewer components likely to fail.)
c) GPU (the 860M is bigger but also older - this might actually turn out to be a tie.)
d) I have a Y50 myself, and I'm actually surprised you can still get them - and with a 4K display, I'd jump on it fast.
The MSI is a very desirable gaming machine with decent specs. But it does seem to be quite shaved down, i.e. a "prices start at" option. That said, it has a newer and more efficient CPU and the GPU, although only 2 GBs, is newer and might actually be just as fast. Then of course, you get a larger screen.
The Lenovo, on the other hand, is probably a special 'fire-sale' offer which may explain the very generous specs. As I said earlier, I'm surprised you can still buy these things. It's a bit like auto makers trying to clear the inventory to make room for a new model by offering 'Classic' versions of the remaining old models... But as a Lenovo user myself, I'd still consider the Y50 a generous and reliable proposition.
From experience, I know the Lenovo will play games like Tomb Raider and GTA V at medium-to-high settings, but not at Ultra or Extreme. I doubt the 2 GBs on the MSI can handle that, even on a Skylake processor. If you're never going to play the abovementioned games (or similar games), the 3-year-old Lenovo model still takes the lead as the best all-round multi-tasker available today.
Best of luck whatever you choose,
GreyCatz.