I have been researching Shinbone Alley in NYC and ended up here.
I remember passing Shinbone Alley somewhere in the East Village.  Searching on the Web, the source of all true knowledge, I could only find three locations that have been identified as Shinbone Alley:
1) going north between 41 and 43 Bleeker St (unnamed in Google Maps but probably a continuation of Jones Alley)
2) going north next to 2 Bond St (labeled Great Jones Alley)
3) running along Washington Pl between University Pl (Washington Sq E) and Fifth Ave (in Washington Sq Park where the fountain is)
Perhaps they are all right, or at least the first two, because I also came across a web page quoting a NY Times article from the 1800s saying the alley went north, turned west and then turned north again.  That fits with my memory which says I saw street signs for it going west off of Lafayette St between Bond St and Bleeker St (labeled Jones Alley) and exiting onto Bond St between Lafayette St and Broadway (across the street from Great Jones Alley on Google Maps) but I need to get down there again to confirm it.  I can see where it might have been composed of what is now labeled Jones alley and Great Jones Alley which would fit with the Times N-W-N description.  
And I just came across this real estate Web site that shows Shinbone Alley running from Great Jones St south to Jones Alley :
http://www.rkf.com/rkf/lease-property-detail-flyer.php?lease_property_id=262

There is another Shinbone Alley on the grounds of Sailor's Snug Harbor on Staten Island:
http://www.mywebdesign.us/snug/wp-content/uploads/2011/05/PLAN_park_map2.pdf
I suspect that one is apocryphal though given it's location between the dormitory buildings and it not extending off the property.