Assuming the same air temp. and humidity levels: If I have an air
compressor pressurizing a 5gal. tank at an altitude of 5,000ft. above
sea level and an identical compressor pressurizing a 5gal. tank at sea
level, will there be a differing amount of air molecules in the 5gal.
tanks?

Yes.  Compressors work against the atmospheric pressure as a starting
point, so the compressed air with be at essentially the same "gauge
pressure" in the two tanks.  Gauge pressure is relative to the
surrounding environment - it is what a gauge reads that measures the
difference between a tank and the surrounding air.

That's right.

At sea level, your atmospheric pressure is approximately 14.17 psi. 
At 5000 feet, it is approximately 12.23 psi.  This is assuming the
standard temperature of 0 degrees C in both cases.

So, at sea level, when your tank gauge reads 100 psi, you actually
have 114.17 psi absolute inside your tank.  At 5000 feet, you have
112.23 psi absolute in your tank.

Therefore, at sea level, you have more air molecules in your tank than
at a given altitude (above sea level, assuming constant temperature).

You can easily prove this to yourself by taking an sealed, empty
(empty means filled with air) 2-liter bottle and driving from Denver
(5280 ft) to Los Angeles (0 feet).  Since the bottle is sealed, no
molecules enter or escape.  However, since the atmospheric pressure
changes, you will notice a decrease in volume.  In other words, the
bottle will appear squished.  And since pressure, volume, and number
of molecules are all related by the equation PV = nRT, where P =
pressure, V = volume, n = number of moles of gas, R = gas constant,
and T = absolute temperature, you can do the math from there.

I think I disagree: The guage will only read about 80 psi at an
altitude of 5000 feet, so the pressure will be about 92 psia instead
of 112 psia. This is because the compressor will draw in fewer air
molecules per stroke in the same number of minutes of compressing.
Alternately the compressor will need to run about 20 % longer for the
gauge to read 100 psi which will make the touf answer correct.  Neil