Daniel Sheehan is accused of planting the bomb as part of a $2 million extortion plot.
Federal prosecutors say he also threatened to explode bombs in three other Home Depots on the island if he did not receive the money.
The 50-year-old is charged in federal court in Central Islip with both extortion and use of a destructive device in the commission of extortion.
His defense attorney denies the device left in the Huntington store was dangerous.
Sheehan worked at a Home Depot in Deer Park.
If convicted, he faces 30 years in prison.
