I don't get to London too often, but it is a wealth of good spots, many very photographer friendly. Main rules being stay out of the way of passengers/crew, never walk beyond the marked lines and don't use tripods or flash.
If you could just pick one, Stratford would probably be the best, get there on a weekday morning and you get a procession of heavy freights, diesel and electric as well as the Anglia class 90 locomotive hauled passenger workings. Photography is good there as well, can stand in a single spot and see almost everything worth seeing.
Clapham Junction is the busiest on the network and does see some freight but not a huge amount, the station is so wide it is impossible to get photographs of everything from a single vantage point. If you get a chance to visit in rush hour it is well worth just watching the volume of trains that pass through. Again never had any problems with photography here.
Wilsden Junction is good for spotting but has pretty poor angles for photography.
Somewhere on the approach to Marylebone would be quite good in the morning for the Class 67 hauled Chiltern trains, can see the whole fleet in about a 90 minute interval.
If you get a chance to get out of town for a day, take the train out of Paddington to Tilehurst for a great selection of freight and mainline passenger trains. Nice quiet rural station.
My advice would be to get a travelcard and just spend the day roaming the different networks out of London, even now there is a pretty big range of variation between the different operators and every major London station has its own charm.