Near as I can tell, the reason for American Samoa's Unorganized status is that there are two regions which has no true county level administrative government. The first is Rose Atoll (the southern most point of the United States territory), which is an uninhabited wild life preserve. The second, Swain Island is privately owned and mostly used as a coconut plantation, though it is presently not permanently inhabited, with the 2010 census recording the last non-zero population of 17 people, though reports of the island's lack of habitation have been found as early as 2008. The island is accorded a single non-voting representative in the American Samoa Territorial Legislature. In addition, Swain Island is disputed territory between the United States and Tokelau, a sovereign dependency of New Zealand (A treaty between the U.S. and New Zealand recognizes the Island as U.S. territory, but the Tokelau flag contains four stars symbolic of the four islands including Swain).
It's likely because of the fact that Swain Island is still disputed, America Samoa is still Unorganized. The term has typically been used for newly acquired territory that Congress has yet to formally create an organized government for through an "Organic Act". The only other way to create an unorganized territory is to have a portion of an organized territory join the Union as a state, leaving the rest of the territory to need a new Organic act create it's now non-existent government. Wikipedia cites the case of the Missouri Territory when the South Eastern Portion was admitted into the Union as The State of Missouri. Usually, the new state held the largest portion of population of the Territory so it took the government of the territory with it so a new Organic Act or Acts need to be written to create the new territorial government (not to mention rename the remaining territory since now a state has it's name). In the Missiouri Territory's case, Congress portions of the unorganazid Missiouri territory were given to Michigan Territory, and the remainder was divided into the organized territories of Iowa, Minnesota, Kansas, Nebraska, Colorado, Dakota, Idaho, Montana, and Wyoming between 1838 and 1886. Prior to it's own organization, the Missiouri territory itself was part of the Louisiana Territory until the state of the same name joined the union.
TL;DR: Likely because of territory disputes over Swain Island with Tokelau preventing the Organic Act for America Samoa from being properly formalized.