There are a few ways to interpret this question. The first is “when was the last time a substantial Native American force attacked an East Coast city in any way, shape, or form”. However, I believe the intent of your question is more akin to “when was the last time a primarily Native American force decided to attack an East Coast city, then led and executed the raid themselves with limited European influence”. I will provide the best answer I can for both questions.
First, the last point in time that a substantial Native American force attacked an East Coast city may be the U.S. Revolution. Though most of Indian country allied with the British, many New England Indians were sympathetic to the Patriot cause. In fact, the residents of Sturbridge Stockbridge were some of the first to answer the call of revolution and joined Washington’s siege of Boston in 1775. Technically, that is a Native American force attacking an East Coast city. Most of the Native Americans fighting in the U.S. Revolution, however, knowing the repercussions of the war would determine land rights, sided with the British, and the heavy fighting occurred along the frontier in New York, Pennsylvania and the Ohio Valley. I do not know if there was a sizeable Native American contingent at the Burning of Washington during the War of 1812, but that might be a last possible place and time for an East Coast city to be targeted.
To answer the second interpretation of the question, when was the last time a primarily Native American force decided to attack an East Coast city, then led and executed the raid themselves, might be 1715 in the Yamasee War. For several decades leading up to the war Carolina traders paid Native American allies to raid for Indian slaves throughout the Southeast. This trade transformed the southeast nations, shattering old chiefdoms, nearly depopulating Florida, and caused substantial disruption that led to the first verifiable smallpox pandemic from 1696-1700. To give you an idea of the scale, slave raiders permeated the southeast, eventually raiding all the way to the Mississippi, and more Indian slaves were exported through Charles Town than African slaves were imported before 1715. Lower end estimates place the number of Indian slaves exported at 30,000-50,000.
In this atmosphere, the Yamasee were allied with the Carolina traders and were chief slave raiders. After the escalation of slaving, the crash of the Florida mission population from slave raids, and the demographic insults of the smallpox epidemic the pool of available nations to raid dried up. The Yamasee, fearing the British would call in debts and turn on them as slaves like they previously did when the Westo wore out their usefulness, were placed in a no-win situation. Additional issues included decreased land access due to rice farming, and the rise of the French in Louisiana as potential allies.
The Yamasee were joined by many Creeks, Catawaba, Cherokee and Santee who were likewise adapting to the changes in the Southeast. The first attacks came along the frontier, as well as English traders operating in Indian land. Carolina refugees fled to Charles Town, where supplies ran low and there was serious talk of abandoning the colony. Estimates hold ~7% of South Carolina’s European citizens were killed in the war, making it the costliest conflict in the early colonies. The tide turned against the Yamasee and their allies in 1716 when the Cherokee decided to attack their traditional rivals, the Creek, and ally with the English.
While there were never any raids directly on Charles Town a map of the conflict shows the battles raged very close to the city. The actual march toward Charles Town was in process, but abandoned, when the Cherokee heard their own towns were targeted and hurried home to offer protection. Even though Charles Town was not directly attacked, the scale of the hostilities, the proximity to the major colonial town, and the very real prospect of abandoning the colony would make the Yamasee War one of the last good options for a conflict seriously threatening an East Coast city.
Edit: Sources
Paul Kelton Epidemics and Enslavement: Biological Catastrophe in the Native Southeast, 1492-1715
Robbie Ethridge and Sheri M. Shuck-Hall Mapping the Mississippian Shatter Zone: The Colonial Indian Slave Trade and Regional Instability in the American South
Alan Gallay The Indian Slave Trade: The Rise of the English Empire in the American South, 1670-1717
Colin Calloway One Vast Winter Count: The Native American West Before Lewis and Clark