I don't know if you are still looking for information, but the estate agent who told your son to avoid East Greenwich clearly does not know the area.
If you are at Canary Wharf, the main thing is to be near the tube or the DLR. Or the river boat if you are loaded and like a scenic route! Personally I prefer the tube, as it's only one stop. It's a bit of a trek to North Greenwich tube from East Greenwich - and not a particularly beautiful one - but it's safe. It's just the pavements alongside busy roads all the way, so most people prefer to get the bus. There are two bus stops on Blackwall lane where all passing buses take you to the station. 5 minute wait would be average (though you get the odd freak 15 minute gap which has us moaning for days!).
The DLR is ok, but the Greenwich stations are near the pricey bits of town - except maybe those flats out towards Deptford (can't remember the name), which personally seem less attractive to me than Millennium Village.
Azof Street is fine. You'd be close to one of the bus stops I mentioned. Trafalgar Road looks a bit run down, but is pretty safe and has useful shops - Co-Op, Dominoes, various other takeaways.
How old is your son, if you don't mind me asking? Somewhere in the new(ish) Millennium Village might suit him if he's young and likely to be out at central London bars/clubs/at friends in other parts of London a lot. It's a shorter walk to the tube and new flats, so low stress!
I live in the area, but don't want to say toooo much on here, so feel free to PM me if I can help at all.