No, Amon is not energy-bending when he takes away someones Bending abilities.
Amon, born Noatok was the son of the crime-boss Yakone, was a highly skilled Blood-bender and brother to the city councilman, Tarrlok. His ability to remove the ability of others to Bend, appeared to be related to his ability to blood-Bend.
As near as we can see, Amon was able to disrupt the chi pathways, perhaps by causing the person to be unable to access the connection to the bending regions of their brain. This use of bending with near surgical skill was unable to be undone by Katara, considered to be the most powerful healer known.
Korra, having lost her ability to Bend to Amon, was unable to access her known abilities of fire-bending, water-bending or earth-bending, but when she was able to, under extreme duress, air-bend, her ability to do so was unaffected by Amon's block. So whatever he is doing, it blocks the known memory of bending or the access to practiced bending in the brain. Her previously untapped airbending ability was unaffected.
Korra was told she would not have access to her previous bending powers and that nothing known could be done to repair her powers.
In a moment of quiet desperation, she had a vision from Aang who suggested that at her lowest point she would be able to be open to the Avatar state and the ability to reach her previous incarnations. Aang shares the knowledge of energy bending and reaches past the block placed by Amon by activating her Avatar State. This restores her bending powers. This also gives her the ability to undo all the damage done to benders by Amon.