I assume that microwave involves rotational energy and Infrared involves vibrational motion. The total energy of microwave radiation may be higher than Infrared radiation.
Infra red is absorbed in a thin layer at the surface; traditional ovens do this - so you can burn the outside but the inside is raw. Having lower absorption allows the microwaves to penetrate some distance into the food, which is a major advantage over ordinary cooking methods. Further, there is no special water resonance at 2,45GHz - indeed the water/sugar/fat content have a big effect anyway - but water molecules are asymmetrical and they rotate in the high frequency field.
I agree with Ian. Penetration depth of infrared radiation is strongly wavelength-dependent and can reach up to some millimeters in soft tissue for IR-A (wavelength = 0.78 to 1.4 μm).