What is the last name of Sacajawea?

Your question is based on a false premise: that native Americans historically had a first, middle and last name just like Europeans or white Americans. This is incorrect. Only under the reservation system in the late 1800s were natives forced to adopt names like those of white people.

The young Shoshone woman you mention was captured by an enemy tribe and eventually traded to the Hidatsa people of the Upper Missouri; they named her Tsakakawia (Bird Woman) - this was her full and complete name. Lewis and Clark misunderstood this native name and recorded it in different ways - the version Sacagawea is perhaps closest to the real name (it was never spelled with a j during her lifetime).