How should I prepare myself for a Master's degree in Computer Science from Stanford or Berkeley? If I am already working as a Software Engineer?
Whom should I ask for letters of recommendation for a Master's degree in Computer Science? 


See if someone remembers you from your undergrad.  You can send an unofficial transcript as an attachment to jog their memory.  Also ask someone where you work, if unveiling your plan to that person isn't too awkward.


  How should I prepare myself before I apply? 


Pick a couple of programs you're interested in applying to. Read the program of studies carefully, then check the courses you would be signing up for in your first year, to see what the prerequisites are. This will guide you in your course selection, and give you a fair view of how well prepared you are. Make sure to look at the textbooks used, to gauge the level of difficulty.

Notes: The cost of living is much lower in a less built up place, such as, for example, Madison, WI; if you get a TAship, which shouldn't be a problem in CS, you won't be paying tuition, and you'll get a stipend, which will cover slightly a frugal but not spartan life, but not many plane tickets to California.  However, if you prefer to stay in CA, I would think there would be plenty of opportunities there.

I'm not sure how fresh the GRE needs to be.  The application instructions should make that clear and if not, you can email your question.  Don't worry about your verbal GRE.  As long as you didn't embarrass yourself (which you didn't), for a CS master's, that doesn't matter; especially since your nonverbal score was strong.  When applying for a geek degree, it's fine to come across as a geek.