Does the PS Vita have better graphics than the 3DS?

"Yes, but it's not a good idea to judge a game based on polygonal count."

To expand on this answer, the PS Vita's screen is 540p, which by some is considered HD, but to others it is Enhanced Definition.

The 3DS's graphics chip isn't as powerful as the PS Vita, and the console plays games at a lower resolution, so if the 3DS were to play games at 540p, the graphical differences would definitely show. Don't let the graphical difference make you change your opinion on the 3DS, as you may like the games on it more than the games on the PS Vita.