Where does the altimeter measure from?
There are a few types of altimeters but they all generally do the same thing and can be calibrated to anything if need be. Where they measure from and what they consider 0 are really 2 different questions.  

A pressure altimeter reads from the pito-static port (many planes have more than one of these for redundancy) and they are generally located forward on the air frame and often on the side somewhere.


((737 static port) source)

Radar Altimeters will most likely mount to the bottom of the aircraft (since that is the way the radio beam needs to go). 


(source)

According to this discussion radar altimeters are on the belly and 0ft is calibrated to mains on the ground, after that altitudes will be read out in negative values. 

And from here


  The callouts (50, 40,30,20,10 feet, etc) is the function of two radio
  altimeters which provide the height of the main landing gear above the
  runway.