I would say Michigan has had much higher highs than Purdue, but Purdue was more consistently good. I would give the edge to Michigan simply from a perception point because Michigan has had a couple of memorable tourney runs, while Purdue has not. If you asked the casual non-Big Ten basketball fan, my guess is that based on those two NC appearances, they would say Michigan.
And actually, across that stretch it's hard to say Purdue was more consistently good, at least until Painter took over. The start of that 2002 and onward stretch was the late days of Keady, with Keady only making the tournament in 2003 and going 1-1 (making 2nd round). Keady's last 4 seasons (2002-2005) were 13-18, 19-11, 17-14, and 7-21, finishing below .500 in conference three of those four years. Likewise Beilein took over for Amaker. So I think you have to rate them based Painter vs Beilein, not on what occurred before that.
Painter had a rough go in 2005-06 with the depleted roster he had, going 9-19 (3-13) his first year, but he's been pretty consistently good since then. Outside of a rough stretch of 2013-14 and 2014-15 seasons (coinciding with some recruiting busts and--not surprised if this had an effect--following his divorce), he's been over 20 wins every season and over 25 wins 7 times.
Michigan is very similar. Beilein took over two years after Painter, and had a rough first year but mostly solid success since. He's had a rougher go in conference play than Painter has (.561 to .617), but as you point out his highs in the tournament have been higher.
I would say they're pretty darn close. How you rate them is more related to whether you are rating regular season and conference finishes more highly, or whether you're rating the tournament more highly.
Conference play, I'd give the edge to Painter. Higher win percentage, more often finishing in the top 3 in conference, etc.
Beilein has been to the tournament 9 of 11 years, Painter has been there 10 of 13 years. Beilein has made the second weekend 4 times, Painter has made the second weekend 4 times. The difference is that all Beilein has made the third weekend twice, and all 4 of those trips for Painter has ended in the Sweet 16. So tournament-wise, it goes to Michigan.