IRAC images are in units of MJy/sr. If you want to convert them into flux density/pixel units, you can convert steradians into arcsecconds squared, and then multiply by the area of the pixel. Remember that in BCDs the pixel area is approximately 1.22 arcseconds squared, whereas in the pipeline mosaic the pixelsize by default is 0.6 arcseconds squared exactly. So, for example, for the pipeline mosaic a pixel value needs to be multiplied by (1E12 micro-Jy)/(4.254517E10 arcsec**2) x 0.6 arcsec x 0.6 arcsec = 8.461595 to obtain micro-Jy/pixel flux densities.
Remember to make all the appropriate corrections to your measurements. These include
1. aperture correction (including point source versus extended source photometry correction)
2. (position dependent) color correction
3. pixel phase correction in channel 1
4. image artifact corrections
5. overlap correction in mosaics
6. background subtraction
7. pixel solid angle correction in BCDs (but not in MOPEX-produced mosaics).
Information on these corrections can be found in Chapter 4 of the IRAC Instrument Handbooks.
Once you have measured the flux density of your source, you can convert from Jy into Vega magnitudes (from a Kurucz model spectrum of an A0 V star matched to the visible photometry of Vega) using the zero-magnitude flux densities posted in Table 4.2 of the the IRAC Instrument Handbook. Note that zero magnitude flux densities are not what you would measure for Vega necessarily, as Vega does have circumstellar dust. If F(i) is your measured flux density and F(0) is the zero magnitude flux density in the corresponding channel, then the magnitude corresponding to F(i) is m(i) = 2.5*log10(F(0)/F(i)).