I'm temtped to say MGS, because overall it's more solid, with Uncharted having some screen tearing and texture pop-in, it also has amazing character models.
On the other hand the character animation in Uncharted is better, with far less strange 'snaps' from one mode to another which always seems to occur in MGS - for example Snake snaps to a wall, Nathan really seems to turn to it and naturally nestle against it.
I believe Uncharted native resolution is higher, too, which is pretty impressive considering (the odd screen tear aside) it features amazing environments. MGS probably has better particle effects but overall I'd say Uncharted features a broader set of overall effects, and has amazing lighting, vegetation, water, etc.
In the end I'll say Uncharted as I find the way it's engine streams levels much more impressive and immersive than MGS's rather small levels with frequent loading between levels.
Try to be reasonable... its easier than you think...
