This is not my Pemberton's-I am helping anyone who might be related. It is assumed by some that James Pemberton of Malden and Charlestown MA was not related to James Pemberton who shows up in Boston in 1646, but they were father and son: Walter Watkins in his 1890's booklet (based partly on a book written 10 years earlier by a woman -forgot her name- titled something like The Pemberton, Ellis, Titcomb families, published in Boston), said the James Pemberton of Malden and the James Pemberton of Boston "must not be confused," but the truth is they WERE related. These authors only had limited access to records, otherwise they did very well with the records they had, and their mistake is also due to the fact that there is no actual "ships passenger" list of Winthrop's Fleet of Puritans who came to MA, only a list compiled using early MA records to figure out who came over with Winthrop in 1630. But when the authors quote records of MA they are very helpful. But apparently neither author knew about the land patent given to James Pemberton in 1628 for land outside Boston, an island which was called Pemberton's Island (name later changed, but early records show Pemberton's Island), and that this land patent shows a connection to BOSTON. This was the James Pemberton who came to MA in 1630 on Winthrop's Fleet as an adult man, James Pemberton and wife Alice, and John Pemberton and wife Elizabeth--these were brothers. John's wife died in 1646 and he went back to England and died Essex co England 1654 per his will which mentions his "brother James of New England." This James of New England--Malden MA- had a SON NAMED JAMES who had been born in England 1622 and when this James (b1622) JR grew up he moved to BOSTON in 1646 and was registered as a freeman there. SO: James Pemberton, wife Alice, and SON James Pemberton came to MA in 1630, and James JR went to Boston in 1646 at the age of 24, and his offspring are the Pemberton's of Boston. A helpful site on this is The Winthrop Society site in "Settlers" and "Adventurers"/Founders lists (outside "links" on the site is not helpful, but the rest of their site is), and also Ancestry.com records. Winthrop's Fleet site in "Settlers" mentions James' children: JAMES, Sarah, Mary, and John.
James of MA SR probably came from Essex England since his brother John's will 1654 was recorded there, and also James had a friend he mentioned in his 1661 will, Joseph Hills, and Hills was from Essex England, and Joseph HIlls was also a fellow Founder of Massachusetts Bay Colony. So, if you want the possible father of James SR (land grant 1628/to MA as adult 1630), he may be found in Essex.
This is all I know of this Pemberton family.