The Vita uses the same configuration of CPU processors as the iPhone 4S and iPad 2/new iPad, just in quad core form (the iPhone/iPad was dual core), and a tweaked MP4+ GPU compared to MP4 on iPad 3.
3DS is rumored to use a dual core previous gen CPU (2 of them actually). Although quite a fair chunk weaker than the PS Vita's latest quad core A9 Cortex, it is still powerful nonetheless, or else it wouldn't drive that much multiplats.
MGS 3D Naked Sample isn't fair enough, but you can tell some 3DS power from there. Resident Evil Revelations is beautiful (and only launched less than a year after launch) and proves that the 3DS system can be a mammoth.
Uncharted isn't really THAT beautiful to be honest. It's a launch title, plus the colors are quite over saturated. I'd choose a full 3D environment RPG released later as comparison instead.