We caught the JR train from Tennoji to Iga-Ueno and then on to Uenoshi which in the end took 2 hours, which was about double the time we were expecting.
It was worth it to visit the Ninja Museum because it was very cool, informative and had we gone on a different day we would have had a Ninja display.
The sort of information I found interesting was how the ninjas were experts at espionage and were effectively spies who took their job very seriously. They would not eat meat or pungent foods that would enable them to be detected by their smell. They also adapted their houses to look like standard farm houses but were in fact set up with traps and hidden weapons. They also told the time using cats eyes!
This really was worth a visit and the surround area had a castle to explore too.
One thing to be aware of is that the trains from Iga-Ueno to Uenoshi do not run as often as other trains in Japan so check when you arrive so you don’t have to wait for an hour like we did.