If you like food, a good way to see the smaller neigbhorhoods of the outer boroughs is to follow some of the posts on chowhound.com's outer boroughs board about neighborhood food crawls in those areas.
Here is the first example I pulled up, but there are many more
Roosevelt Ave Mexican Survey - Outer Boroughs - Chowhound
there's also a good one
My Google Map of Obscure Street food in Eastern Jackson Heights - Outer Boroughs - Chowhound about mapping all the great street food vendors in eastern jackson heights.
I have heard that there's great food in carts at the Red Hook ballfields in Brooklyn - that would be a cool, highly industrial neighborhood to check out - by the water. Though now that Ikea is moving in, not sure what the nabe is like.
You could also do a gallery walk in Williamsburg (make sure you check which days they are open as many are only Thursday -Sunday or something) and afterwards go to one of the uberhip cafes or restaurants.
You could also search the archives of the NY Times for articles about "living in" in the real estate section, as they often cover neigbhorhoods that are not that well known.
How about the trolley tour of the South Bronx galleries and artist studios? It's an iffy neighborhood but the trolley tour is fun and off the beaten track.
I think the Steinway factory in Astoria Queens used to give tours = you could check into that, though that may be old info.
I think it's good to have one destination in a neighborhood (a restaurant or factory or gallery or whatever) and then use the opportunity to walk around.