OK, I added some missing pieces and this should be my final update:
State bests for the Mile for Men:
Outdoors:
MA: 3:56.82 by John Jefferson on 9 Aug 2008 at Falmouth MA
TN: 3:57.16 by Matt Elliott on 1 Jun 2013 at Nashville TN
VA: 3:57.46 by Josh McDougal on 31 Mar 2007 at Lynchburg VA
NC: 3:54.57 by Kyle Merber on 5 Aug 2016 at Raleigh NC
ME: 3:58.57 by Daniel Hill on 4 Jul 1998 at Brunswick ME
AR: 3:59.70 by Jason Bunston on 1 Apr 1995 at Hot Springs AR
OH: 3:58.4h by Steve Heidenreich on 23 Jul 1975 at Berea OH
AZ: 3:56.4h by Paul Cummings on 16 Mar 1974 at Tempe AZ
LA: 3:57.8h by Hailu Ebba on 9 Jun 1973 at Baton Rouge LA
GA: 3:59.06 by James Igohe on 20 Jul 1984 at Atlanta GA
FL: 3:58.8h by Barry Brown on 13 May 1973 at Gainesville FL
KS: 3:53.3h by Rick Wohlhuter on 31 May 1975 at Wichita KS
Other: 3:43.13 by Hicham El Guerrouj on 7 Jul 1999 at Roma
CA: 3:51.1h by Jim Ryun on 23 Jun 1967 at Bakersfield CA
IL: 3:54.23 by David Krummenacker on 25 Jul 1998 at Edwardsville IL
NY: 3:55.19 by Tim Hacker on 22 Jul 1989 at New York NY
TX: 3:58.72 by Julius Bor on 5 Apr 2008 at Austin TX
WI: 3:56.38 by Matt Tegenkamp on 6 May 2006 at Madison WI
OR: 3:47.32 by Ayanleh Souleiman on 31 May 2014 at Eugene OR
SC: 3:57.70 by Michael Hammond on 12 Apr 2014 at Greenville SC
PA: 3:53.2h by Tony Waldrop on 27 Apr 1974 at Philadelphia PA
MO: 3:56.10 by Duncan Phillips on 5 Jun 2014 at St. Louis MO
IA: 3:57.55 by Phillip Lagat on 24 Apr 2010 at Des Moines IA
MI: 3:56.77 by Mac Fleet on 10 Aug 2014 at Saline MI
NJ: 3:59.5h by Jim Norris on 23 Jun 1990 at Holmdel NJ
Indoors:
MA: 3:50.92 by Galen Rupp on 26 Jan 2013 at Boston MA
IN: 3:55.33 by Kevin Sullivan on 11 Mar 1995 at Indianapolis IN
Other: 3:48.45 by Hicham El Guerrouj on 12 Feb 1997 at Gent
CA: 3:51.8h by Steve Scott on 20 Feb 1981 at San Diego CA
VA: 3:57.41 by Julius Achon on 22 Feb 1997 at Fairfax VA
NE: 3:59.70 by Kevin Batt on 21 Feb 2014 at Lincoln NE
AR: 3:49.89 by Bernard Lagat on 11 Feb 2005 at Fayetteville AR
GA: 3:55.84 by Paul McMullen on 28 Feb 1998 at Atlanta GA
WA: 3:53.89 OT by Izaic Yorks on 27 Feb 2016 at Seattle WA
OH: 3:57.11 OT by Clayton Murphy on 6 Feb 2016 at Akron OH
TX: 3:55.02 by German Fernandez on 28 Feb 2009 at College Station TX
PA: 3:57.86 by Sam McEntee on 28 Jan 2012 at University Park PA
MI: 3:59.82 by Ben Reese on 14 Feb 1997 at Ypsilanti MI
NY: 3:50.63 by Matthew Centrowitz on 20 Feb 2016 at New York NY
IA: 3:56.84 OT by Jordan Williamsz on 15 Feb 2014 at Ames IA
KY: 3:58.60 OT by David Freeman on 2 Feb 2008 at Lexington KY
FL: 3:58.52 by Tom Lancashire on 2 Mar 2006 at Gainesville FL
NJ: 3:49.78 by Eamonn Coghlan on 27 Feb 1983 at East Rutherford NJ
Doesn't knock off any more states that I can tell, unfortunately.