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Also, the first epidemics entered the continent from the Gulf Coast in the mid 1500's, I do not find it unbelievable that the epidemics killed a large percentage in the St. Laurence valley before 1600.

While you may be correct in your first supposition (that disease hit the Mississippian tribes earlier), your second is wrong. The Hurons, Neutrals, and Iroquois were not coastal tribes like whoever occupied the Plymouth site. They were also not strictly St. Lawrence Valley tribes. They were inland and didn't have their first contact with Europeans until the very late 16th century/early 17th century. When the first explorers and missionaries made their way out there, they found thriving towns and no trace of the dread diseases which would come later. It is upon their estimates that the population numbers are based.

There is plenty of excellent primary source material on this subject if you want it. The Voyages of Samuel de Champlain, The Jesuit Relations 1609-1673 as compiled by Reuben Gold Thwaites, and Sagard's History of Canada and the Voyages of the Recollect Fathers are all good sources for population numbers and agricultural information.

Just because the tribes you mention we not coastal tribes does not mean that they were spared from the dread diseases. Look at the way the Black death swept through Europe. The black death was first reported by European sources on the Black Sea. London a major river port in the North of Europe was hit by several waves of disease, while the disease killed over of 1/3 of the entire population of Great Britain. Just because a village was not on the coast did not mean that it was spared; many of the villages and towns abandoned in Europe at this time were inland.

I would expect that epidemic disease would have followed the trade routes inland and destroyed a great many marginal villages and lead to the military extermination of many tribes that were significantly weakened. The Sioux (Dakota) lived near the shores of Lake Michigan in the early 1700's they moved into the great plains after acquiring horses and the tribes to their west were greatly weakened relative to the Sioux by diseases that the Sioux had greater resistance to, having been exposed earlier.