They're both works of historical fantasy set in Feudal Japan, but that's about it. They don't take place in the same universe, though I suppose it's entirely possible that they could and it wouldn't effect either story.
Ninja Scroll is presumably set during the period in which the historical Jubei disappeared from recorded history and is thought to have wandered the land accomplishing brave deeds and such. No specific year is given, but this would have been between 1631 and 1647. Since the movie establishes Jubei's previous run-in with Genma as having taken place five years earlier, I would wager that Ninja Scroll takes place no earlier than 1636 or so.
Princess Mononoke is also set during a historical time period, specifically between the decade of 1467 to 1477, around the war of Onin, according to the official FAQ. It was a much more dynamic and confusing period of Japanese history, before class structures were as rigidly defined. Miyazaki saw it as a time when man's relationship with nature changed in Japan.
By the time Jubei departs on his journey, the world is much more closed than it would have been in Ashitaka's day, and the forest spirits have long since vanished and the world is a much darker place. It certainly occupies a place on the cynical end of sliding scale of Idealism versus Cynicism (look it up at tvtropes), whereas Princess Mononoke was somewhat melancholy, but more hopeful.
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