Fall - Winter is the best time to dive in Monterey Bay Area.
From my experiences the water is actually warmer in the Fall - Winter months. My warmest dives in Monterey / Carmel have been in October 2002 (52 - 53 degrees) and November 2001 (57 degrees), while my coldest dives in the area have been in May 2002 and May 2003 (48 degrees). We have all heard stories about 41 degree water, but I haven't hit that yet. (I am sure that we will hear from others that have)
The general rule of thumb that I have heard is that we are about 10 degrees cooler than the San Diego area. (no data, merely anecdotal hearsay)
The air temps are a little cooler out on the water in the winter months, but that just makes the temperature difference less. You just need to be prepared for cold boat rides and SI.
I have always heard that the visibility is better (in general) during the winter months when the currents change and the air temps are cooler. I have never really compared the vis based on time of year. The vis usually gets slightly better as you head south from Monterey. The temps are usually cooler and the vis a little better as you get down by Carmel and Pt Lobos.
Be prepared that 30 - 40 ft visibility is generally considered very good for the area, and less than 25 feet is common. However, there is usually so much to see within 10 feet of you that you may not care that you can't see 75 feet away. (again I am speaking in general terms from my experiences)
Personally I think it is great to dive Monterey any time of the year, and I just wish that I had the time to dive more often.
my dos centavos, but only because you asked.
Wristshot
[it is sad that I feel so compelled to include so many disclaimers to minimize the risks of getting flamed --*deep sigh*--]