I would say Michigan or Boalt. Duke isn't on the same level. Take a look at the SCOTUS clerks selected this year. You will see that no Duke students were selected. Apparently the Supreme Court doesn't consider Duke to be very prestigious. Michigan and Boalt have much better reps and will provide much better options throughout the country.
That doesn't follow. Students from Cardozo and UGA were selected. Michigan and Duke had zilch. Does that mean Cardozo and UGA are more prestigious than Mich and Duke. Your suggestion seems to imply this...
Here's the list:
OCTOBER TERM 2007 SUPREME COURT CLERK HIRES (as of March 23, 2007)
Chief Justice John G. Roberts
1. Jason Burnette (UGA 2006 / R. Lanier Anderson)
2. Josh Hawley (Yale 2006 / McConnell)
3. Anton Metlitsky (Harvard 2005 / Garland)
4. Erin Morrow (Yale 2005 / Wilkinson)
Justice John Paul Stevens
1. Todd Gluth (Boalt Hall 2005 / W. Fletcher)
2. Sara Klein (Cardozo 2005 / Barry (3d Cir.) / Lifland (D.N.J.))
3. Kate Shaw (Northwestern 2006 / Posner)
4. Abby Wright (U. Penn. 2006 / Boudin)
Justice Antonin Scalia
1. Aditya Bamzai (University of Chicago/Sutton/OLC)
2. John Bash (Harvard 2006 / Kavanaugh)
3. Bryan Killian (Harvard / Niemeyer)
4. Rachel Kovner (Stanford / Wilkinson)
Justice Anthony M. Kennedy
1. Michael Chu (Harvard / D. Ginsburg)
2. Stephen Cowen (U. Chicago / D. Ginsburg)
3. Andrianna ("Annie") Kastanek (Northwestern 2005 / Ripple)
4. C.J. Mahoney (Yale 2006 / Kozinski)
Justice David H. Souter
1. Bert Huang (Harvard 2003 / Boudin)
2. Leslie Kendrick (UVA 2006 / Wilkinson)
3. Michael Mongan (Stanford 2006 / Garland)
4. Micah Smith (Harvard 2006 / Calabresi)
Justice Clarence Thomas
1. Eric McArthur (Chicago 2005 / Luttig)
2. Carrie Severino (Harvard 2005 / Sentelle)
3. Heath Tarbert (U. Penn 2001 / D. Ginsburg)
4. Leila Thompson (NYU / Lambert (D.D.C.) / Sentelle)
Justice Thomas, by the way, is almost done with his October Term 2008 hiring. See here.
Justice Ruth Bader Ginsburg
1. Ruthanne Deutsch (Georgetown 2004 / Dyk (Fed. Cir.))
2. Brian Fletcher (Harvard 2006 / Garland)
3. Tom Saunders (Yale 2004 / Leval)
4. Zack Tripp (Columbia 2005 / Kearse)
Justice Stephen G. Breyer
1. Michael Bosworth (Yale 2003 / Rakoff (SDNY) / Katzmann)
2. Karen Dunn (Yale 2006 / Garland)
3. Eric Feigin (Stanford 2005 / Wilkinson)
4. Philippa M. Scarlett (Columbia 2003 / A. Williams (7th Cir.))
Justice Samuel Alito
1. James Hunter (Yale 2004 / Alito)
2. Geoffrey Michael (Yale 2000 / Alito)
3. David H. Moore (BYU 1996 / Alito)
4. Jessica Phillips (Northwestern 2006 / Flaum)