I went through this last year before I bought my 44 lever action.
I ask my experienced gunsmith his opinion on things, and he's never led me wrong. He said I could go Marlin or Winchester, as either one was fine. I polled some experienced gun owners I trust, and some leaned one way and some the other, perhaps with a slight preference for the Marlin. I was told how Marlin makes different rifles for different cartridges and how the Winchester rifle action is excessively long for pistol cartridges. I was told that the Marlin was better because you can mount a scope. In the end, I got the Winchester Trapper because Marlin no longer made the short 44.
The scope mounting issue is moot since the Winnies have been angle eject for years now. On the plus side for the Winchester, the long action probably allows longer bullets than perhaps the Marlin does, and the larger action opening is probably easier for single-feeding cartridges or clearing jams. (Not that the Winchester has a jamming problem, but I've tried some goofy bullets in there.) And the wood on the stock I got was absolutely amazing. Nearly everyone who sees it comments on the wood.
The only really frustrating thing on the Trapper is that the front sight dovetail is directly behind the barrel band and really limits the front sight options. I want a gold bead, but the only one that will fit is the Lyman, the bead fell out the first time I shot it, and my 'smith said it was a loose fit, so I returned it and am not excited about trying another.
I initially put a Williams 5D aperture sight on it (although wish now I had sprung for the FP), and intend to mount a scout scope to it with the XS Sight Systems mount.
I'm not sure how the Marlin safety is mounted (I'm too lazy to bring up their web site), but I find the tang safety on the latest Winchesters to be more intuitive to use than the cross-bolt on the older models, but I was disappointed to find out that Marble's has no tang sight for the tang-safety 94 (yet - they do for the tang-safety 1892.). That's only an issue if you want a tang sight.