I'm voting for something from the early Mass. Bay Colony.
That flag would be referred to as a "red flag with a white canton with a red cross in it" and in searching for that I found a reference that "In 1636 a famous sermon was preached in Salem, Massachusetts by Roger Williams (who was later banished and became the founder of Rhode Island) which stated the cross was a symbol of popery and was therefore the symbol of the antichrist. The Governor of Massachusetts Bay Colony, John Endicott, fearful for his soul, subsequently ordered the cross removed from the flags used in Massachusetts. "
IOW, the early Mass Bay Colony flag matches the exact one flown on that boat. The red cross in the canton being removed in 1636. The general pattern (red flag with white canton) would be English Navy or early New England derivatives apparently.
So...what replicas does that leave recently afloat?
The Jamestown flags supposed had red and white stripes in the main field, per Ship replica - Wikipedia, the free encyclopedia
. (This flag doesn't show there.)