Yaquis (northern Mexico) against the Spanish: First expedition in the late 1520s or early 1530s (can't remember which). Spanish said that they won the ensuing battle, but promptly turned around and headed for home. It's been a while since I read up on this, but from old and possible faulty memory the Yaquis requested missionaries in the 1560s but were still rebelling as late as the early 1900s.
The Southeastern US. DeSoto wanted to settle in some areas along the Mississippi where the Mound-building cultures were still strong, but by that time his expedition had been worn down enough that the local Indians were too strong for him to control them. The Spanish made several other attempts to settle the interior Southeast, all of which failed. (DeLuna Expedition, Juan Pardo expedition in conjunction with the Spanish settlement in Florida (1560s). The Indians of the interior southeast lived another 120-150 years with minimal European interference, though they almost certainly suffered a series of epidemics that spread from the Spanish colony in Florida.
Canadian Indians in the 1520s or 1530s against the French--though I'm not sure the issue was a rebellion there.
Haiti, though that was an oddity in that the rebels were colonists too, though of a voluntary sort.
If you count runaway slave enclaves, there were quite a number of long-lived ones in South America.
Chichemics (wild tribes along the border with the 'civilized' parts of Mexico) held their own for around 50 years.
Jivaros: The Spanish apparently conquered them at one point, were tossed out, and didn't come back (probably because it wasn't worth the effort)
The Neo-Inca state established after Manco Inca's rebellion fell a little short of your 50 years, but it came close.
Virginia: Well sort of. The Spanish attempted a mission settlement which failed. I think that was in the 1570s. Depending on when you figure the Powhatan Indians were conquered that either falls just short of 50 years or is a bit more.
Hope that helps.