My bike commute is thru the Far Rockaway's, but in 10 years I have NEVER had a negative encounter with local residents. Possibly as I'm south of the A train subway tracks and away from the projects (by a block). For a few years - when the Marine Parkway bridge was under repair, I commuted due east thru Brooklyn thru 2 areas with housing projects and never had a problem in these area's either.
Your route could be a block from a troubled corner and you might never know there's a problem. You also might well be a target for a robber using a car while a block from your home. Recall the incident in Lynbrook a few years back where some gang members robbed and killed a guy in his yard after he had just walked home from the LIRR (in a nice neighborhood).
I agree with others that a bike commuter seemingly is a fleeting target and not the "usual" kind of target for a mugging. Pedestrians and cars stopped at lights seemed to more favored.
I would certainly drive the route a few times at the times you expect to be riding thru to get a feel for the area.
FWIW, It would be fine by me if my commute was extended from 10 miles to 15 or 17 (extending up into the Wheatley Heights/Dix Hills area as others have suggested), it just takes a bit more time and it's all time on the bike.
SB