Jonathan, the Bay Area apartment market does experience lower cap rates compared to other regions, but you're wise to still consider investing here. Remember that cap rate represents return for one point in time. It's not an overall return so it doesn't paint the overall investment potential. Contrary to the residential housing market, apartment is the hottest commercial property sector in the Bay Area currently and across the US. You may have recently heard from local TV news and articles that rents are not only rising here, it's outperforming other markets. So what does this mean if you own an apartment here?
Let's take for example Santa Clara County which has experienced 13% rent growth over this past year. If you had owned a 6 unit apartment with rents previously at $1,200, your total gross rental income (absent of vacancies) would be $144,000. With 13% growth, your new gross income is $162,720, a increase of $18,720. If the property sold at a 5 cap with expenses at 40%, you just realized an additional $224,640 of capital in one year just from rent growth.
There's a reason why cap rates are lower here in the Bay Area, and it can't be understood by looking at a single number.