Not personally, of course, but during the Revolutionary War, he did order several expeditions against the Haudenosaunee - the Iroquois Confederacy. In particular, the one you're likely thinking of here is the Sullivan Expedition in 1779, which specifically targeted the Seneca. Here is the order that Washington sent to General Sullivan:

The Expedition you are appointed to command is to be directed against the hostile tribes of the Six Nations of Indians, with their associates and adherents. The immediate objects are the total destruction and devastation of their settlements, and the capture of as many prisoners of every age and sex as possible. It will be essential to ruin their crops now in the ground and prevent their planting more.

I would recommend, that some post in the center of the Indian Country, should be occupied with all expedition, with a sufficient quantity of provisions whence parties should be detached to lay waste all the settlements around, with instructions to do it in the most effectual manner, that the country may not be merely overrun, but destroyed.

But you will not by any means listen to any overture of peace before the total ruinment of their settlements is effected. Our future security will be in their inability to injure us and in the terror with which the severity of the chastisement they receive will inspire them.

The Sullivan Expedition rampaged through Seneca country in what's now western New York through the summer of 1779, destroying some 40 towns and villages and creating thousands of Seneca refugees.

Now, there's a common misconception that this and related campaigns against the Haudenosaunee is how Washington got the Iroquoian name Conotocaurious - The Town Destroyer. While his Iroquoian name did take on a new relevance after these events, this wasn't the origin of the name. He had inherited the name from his great-grandfather who had fought alongside the Haudenosaunee against the Susquehannock in the 1670s.