As AndyEastMids mentioned weekends are quiter than weekdays. Monday would be your best bet if you can get a day off provided weather is good. I have shot all day on several occassions and you do get a major rush in the morning with lots of departures and arrivals then it goes quiet until lunch time. Then things kick off in the afternoon and early evening. However you do get a trickle of biz jets and sometimes unusual one of aircraft throughout the day.
If you walk along the glass tunnel leading out to the airport carpark, you can get interesting side shots of aircraft taking off and landing from the chainlinked fence walkway along the carpark itself, more so when you have an easterly breeze, but once the aircraft have touched down you do lose the landing gear, as mentioned earlier.
Shooting near the bridge with a westerly breeze at the East end of the runway is very good as you are looking down on the runway and you have a clear view of the CBD in the background. It takes about 20 minutes to reach from London City Airport.
As far as shooting at ground level near the runway at the East end is concerned I have shot there but, the Police must have had a quiet day, or Pilots lining up on the runway must of mentioned seeing me taking photo's to ATC, because 2 Police vehicles arrived and several officers got out, approached me and said taking photo's here was not permitted, so I left.
If you have a Easterly breeze you can get good arrival shots near the round about as well at the other end. If you arrive by Docklands Light Railway it takes about 5 minutes to walk to this spot.