Caveat: I have never owned or handled a Winchester 94, so take everything I say with that in mind.
First off, be aware that the Winchester 1894 and Marlin 1894 are not the same class of rifle, and the comparison is a bit apples-to-oranges. The Winnie is a full-size action that can handle 30-30+ class cartridges, as well as pistol cartridges. The Marlin 1894 is purpose built for pistol cartridges and is a more compact action. The more accurate comparison would be between the Winnie and the Marlin 336.
Regardless, if the choice were between a post-64 Winnie and a Marlin, I'd take the Marlin hands down. The basic design has not changed much over the last 50 years, and has mainly been cosmetic. The Marlin is a well-built rifle with solid machined parts, and although the new (post-83) guns have a crossbolt safety, it isn't obtrusive and can easily be replaced/deactivated if you want.
If you're contemplating a pre-64 Winnie vs a Marlin, then it really does come down to aesthetics and personal preferences. I went with the Marlin because I liked the solid top receiver for ease of scoping and the simpler mechanism. The Marlin is a dream to tear down: one screw and the finger lever and bolt pop out. Once you've taken a Marlin apart, you'll find that there aren't many moving parts and only a couple of critical interfaces. As a result, it's pretty easy to debug timing/jamming issues.
My best advice would be to look at the used gun market (that's a given for the Winchester since it's no longer in production). There are lots of nice Winchesters that I've seen for sale, and a fairly regular amount of Marlins. As much as I like my Marlins, I'm disturbed at how much new ones have increased in price. They are a wonderful gun, and used to be a bargain compared to bolt action rifles, but that's not the case any more with most Marlins in the $700-$900+ range. I'd have to think long-and-hard about dropping $$$ for a new one. Hopefully, the prices will sort themselves out and the choice won't be so hard in the future.
I love my Marlins (6 and counting), so each his own.