Does the presence of miracles in documents such a the Gospels mean that they are lacking in historical value?

One of the problems is that most of our ancient histories have some mention of the miraculous and we are not prepared to reject all those histories.

Of course when we read those histories, we probably do not take the miracles seriously. Does that mean that what we need to do is emulate Thomas Jefferson and remove all of the supernatural from the Bible?

It is not obvious that we live in a purely naturalistic universe. The percentage of the world population that completely rejects the supernatural is quite small. Why can’t miracles be possible?

A resource I would recommend is Craig Keener’s two volume work on Miracles. He deals with miracles from a biblical and historical perspective, as well from more modern testimonies. It is something to think about.