"Lone Wolf & Cub" is still a work of fiction, even though it is based on history. If you really want to learn some real facts about Edo Japan, I recommend for starters "Everyday Life in Traditional Japan" by Charles Dunn as a good introduction. And if you are into spies, ninjas, and espionage, you should read "Kempei Tai: A History of the Japanese Secret Service" by Richard Deacon.
You said well, "Lone Wolf & Cub" or "Kozure ookami" (子連れ狼) is a fiction, so it's not a history research work. Actually my intention was to show some aspects of the samurais and ninjas in the imagination and art of Japan. Despite the fact of the highest levels of social hierachy have been ocupied by the warrior class, Edo period was peaceful in comparison with early eras (but the peace was maintained by repression). So, saying that one can learn history of Japan from mangas and novel books is same to say that one can learn American history watching western movies.
My father (born in Japan) likes to watch VHS of Japanese TV shows about Edo period (jidaigeki). Owing to him, I know "onihei hankachou" (鬼平犯課帖), "mito koomon" (水戸黄門), "zenigata heiji" (銭型平次 ), among others shows. And I have read novels of Shoutarou Ikenami (池波正太郎) located in Middle Age Japan, an amusing reading (I am not recommeding it to all because these books are in Japanese

).