Found this snippet on GENUKI :-
Sir Henry(4th Baron) married first Philippa, daughter of Sir Guy de Brien, and secondly Joan, widow of Edmund, Duke of York; but, having no issue by either wife, he was succeeded by his brother, Sir John le Scrope, to whom the barony and estates, forfeited by Sir Henry's attainder, were restored. Sir John stood high in the royal favour, and was sent on confidential and diplomatic missions to several foreign courts. Henry VI., in the tenth year of his reign, appointed him to the exalted office of Lord High Treasurer of England. He was buried in St. Stephen's Chapel, York, beside the body of his first wife, Elizabeth Greystock. His second wife, Elizabeth Chaworth, of Wiverton, by whom only he had issue, survived him, and took the veil a month after his death. He was succeeded by his third and eldest surviving son,
Sir Thomas Scrope, fifth Baron, who appears to have led a quiet and uneventful life. His wife is supposed to have been Elizabeth, daughter of Ralph, Lord Greystock, by whom he had issue four sons and three daughters. Thomas, the eldest, succeeded his father whilst still a minor. He was one of the Commissioners of Array for the defence of the Marches of Scotland, and was summoned to parliament from 1482 to 1492. He died in 1494, leaving, by his wife, Elizabeth Neville, daughter and heiress of the Marquis of Montacute, an only daughter, Alice, who married her relative, Lord Scrope, of Bolton. She inherited the estates, but, dying in 1501 without surviving issue, the barony and estates devolved upon her uncles, Henry, Ralph, and Geoffrey, in succession. Geoffrey was a Carthusian monk, and was consequently never summoned to parliament. With him terminated the male line of the Scropes of Masham and Upsall; the estates were divided among his three sisters, and the title fell into abeyance. In the partition, Mashamshire fell to the share of Margery, wife of Sir Christopher Danby, Knight, of Farnley and Thorp Perrow, and who, in right of his wife, became Lord of Mashamshire.
From what i can remember, the Scrope family where well-connected with Richard of Gloucester when he was Warden of the North & were certainly Yorkists at that time, being closely related to both Catesby & Lovell.
This link :-
suggests the family leant towards the Yorkist party for some time, although veering from that allegiance by supporting Warwick's rebellion against Edward IV. However, Eddie did pardon him & he later went on to fight for Richard III at Bosworth & also supported the Lambert Simnel revolt, besieging York with John, Lord Scrope of Bolton in the belief that the city would support a Yorkist cause.
I think we can safely say he was of the Yorkist faction!