First, we need to cut a few years off of "peaceful and stable era". It's true that Ieyasu received the Shōgun title in 1603 and Yoshinobu "returned it" to the Emperor in 1867 (and surrendered himself after retreating from the battlefield in 1868). But the Edo Bakufu wasn't built in a day. They still had to destroy the Toyotomi clan in 1614-15, and crush the Shimabara Rebellion in 1638. And neither was it destroyed in a day. The Imperial-sanctioned Sonnō jōi in 1863 caused a war between the Imperial powers and Chōshū and Satsuma, the first Bakufu campaign against Chōshū, and for Mito to descend into widespread civil unrest. Even before that, the sonnō jōi movement had been causing significant problems, such as the assassination of Bakufu Elder Ii Naosuke in 1860.

So if we narrow the time period down to 1638 to 1863, what then? Then it becomes how you define "peaceful and stable". Riots happened during the Edo, with surprising regularly (Japan is a big place with lots of people), especially in times of hardship (famines, debt, disasters). Does a mob which gathered to demand tax relief, smashed and burned store fronts, and clashed with troops, only to disperse on hearing that their grievance have been solved, count as an uprising or civil dispute? What about a foiled assassination attempt of a Bakufu Elder by a bunch of disgruntled rōnin?

These things all happened, so the Edo period, even limited to after Shimabara Rebellion and before the Shimonoseki Campaign was definitely not 100% peaceful. But I doubt there's ever been polity of at least Japan's size and population that was 100% peaceful over a period of over 200 years.

Perhaps more importantly, during those 200 or so years, there was no widespread warfare (or really any warfare if you don't count the occasional riot and uprising) and no widespread death and destruction that accompanied war. In the Sengoku, daimyōs often raised armies at a rate of 4 to 6 men per 100 koku they controlled. But during the Edo, the legal requirement for troops to be raised was barely over 2 per 100 koku. And as society transitioned from warfare to peace, so did Bakufu policy, going from disallowing daimyōs from hiring rōnin to encouraging it, encouraging samurai to take up civil and administrative pursuits instead of martial. Even Edo Castle's keep, which burnt down in 1657, was not rebuilt, on account that it was a waste of money when there's no war to fight.

Just to give my own personal view on the question. Was there uprisings and violent civil disputes in the Edo era? Yes. Was it a peaceful and stable era? Also yes.