I did this fairly regularly last year and the year before: Waterloo to Canary Wharf.
The Boris bikes are pretty useless, as you have to wait a long time at peak for one. Luckily there is an orderly queue, but sometimes you have it takes two vans full of bikes before you can get one. The situation is probably much the same for going the other way, but I never tried that. Certainly getting a bike from the City back to Waterloo is nearly impossible after 7pm: the racks are empty in the city and they don't bother refilling them as the first commuters in the morning will do that.
Public transport is also pretty hellish: on my first day it took an hour to get from the underground barriers at Waterloo to Canary Wharf. There were problems on the line, so they kept people of the platform to reduce overcrowding, and when you eventually let you on the platform, you join a queue of 4 people at one of the doors; then you find that the trains coming in are so crowded, that not every train had room for one person, so it's still 6 or 7 more trains till you can board. After that, I changed to a bike but used public transport again on that Friday, and had similar problems getting to London Bridge from CW, and eventually went east to Greenwich as the quickest way, as no one was allowed onto DLR west bound or the tube station as the platform is full.
This doesn't happen every day, but I think it would happen at least once a fortnight. Note you can also get from Waterloo by crossing the river, and catching district line to tower bridge and then the DLR, or Waterloo & City to Bank and then DLR, but if one of these is congested, then they all are.
So cycling it is! Not perfect, but definitely the best. There is not a great route between these places, and I had 2 head on collisions with other cyclists on CS2 but it was mostly ok. Here is two of my routes, and note that I am a slow cyclist
http://app.strava.com/activities/12098417
http://app.strava.com/activities/12098347
I'd start with a decathlon cycle. They are pretty decent, and nice and cheap. You'll soon want a brompton (probably) and the CW
Evans has them stacked up by the door. (my folder is a mezzo, and I like that). The hoptown is a bit unwieldy, so getting it to your desk is probably the biggest problem, but most CW offices have secure parking underneath, so you could leave a lock there if that's a better option.
hth