Just tried a place that was recently mentioned in a NY Magazine piece on Frankfurters.
Sparky's Dogs on North 5th Street off of Bedford Avenue.
Milk shakes made with Ronnybrook Ice Cream!http://www.ronnybrook.com/
Hot Dogs made with Niman Ranch meat http://www.nimanranch.com/
and furniture by Salvation Army. Seriously, this place is dog ugly (no pun intended) but the food is artisnal.
DON'T FORGET TO TRY THEIR GRILLED HAM AND CHEESE SANDWICH!!!
135A North 5th Street