The altitude appears to be above ground level. From FAA Order JO 7110.65W Air Traffic Control:
Section 4. Fuel Dumping
9−4−3. ALTITUDE ASSIGNMENT
If an aircraft is dumping fuel in IFR conditions, assign an altitude at least 2,000 feet above the highest obstacle within 5 miles of the route or pattern being flown.
The wording says 'above the highest obstacle', indicating AGL. The CAA Manual of Air Traffic Services is much more explicit:
13.3 Controllers are to recommend to flight crew that jettisoning of fuel should be carried out above 10,000 feet agl. Exceptionally, if fuel dumping at this level, or over water, is operationally impracticable or inconsistent with safety, fuel may be jettisoned above 7000 feet agl in winter and above 4000 feet agl in summer.
This indicates that the altitude requirement of dumping fuel is from the from the first consideration i.e. it takes x feet for the fuel to fall before it evaporates. Swiss regulations go into this at a little bit of detail.
Generally, air masses are only moved vertically very slowly, usually at a settling rate of approximately 60 centimetres per second. In addition the upper limit of the planetary boundary layer (PBL) at the altitude of
approximately 3000 ft over ground renders the air flow from the upper to the lower layers more difficult. Therefore the chance that even a small quantity of fuel reaches the ground is estimated to be unlikely.
Again, it says 'above ground' indicating AGL.