Are SMD packages of microcontrollers (to be more exact : AVR mega series) less affected by noise rather than DIP packages?
Or the opposite is true?
By noise I mean anything that can disrupt the performance of the microcontroller.
It becomes a problem with larger clock frequencies. All high speed devices try to minimize the lead length of the pins and either use QFN or BGA packages which have absolutely no leads. The external leads create parasitic capacitance between pins, as well as increased inductance. Both of these, as evident in their equations become a larger factor at higher speeds.
For the AVR Mega series, it's not a problem, but is most definitely a problem for anything with larger than a few hundred Mhz clock and you'll very rarely find a components with those speeds in DIP.
If mechanical stress conforms to your definition of "noise", then DIP-based designs will be more prone to failures, mainly because of the greater mass of the components and the device as a whole. Also, DIP-based designs will pick more EMI noise, due to both the increased pin length and longer PCB traces.
Other than that, it's essentially the same chip in a different package, so there is no reason for the electrical characteristics to be different.