No they are lower. The 9 bay area counties have a lot of diversity from San Jose which is on the southeastern tip of the bay to Sausalito on the northern end. From rough patches in East Palo Alto to gated communities in Portola. Things that affect prices: schools, commute, amenities (near the woods, libraries, county services, etc), and micro-climate (farther south is a lot warmer than closer to the water).
Single family home rents vary a lot based on school districts.
If you don't have school age kids, you can get something in most parts of the bay for $3500, but the schools are very medicore (and probably terrible compared to most other parts of the east coast or midwest).
If you need good schools, bump your budget up to $4000-4500. You might find a deal somewhere, but it's rare.
When I first moved to the Menlo Park/Palo Alto area two years ago, rent on a decent two-bedroom apartment was around $1400-1700 per month. Currently (two years later roughly), it's $2350+ a month and still climbing.
In fairness, a lot of that has to do with Facebook moving into Menlo Park and the crazy demand for space in Palo Alto / proximity to Stanford University.
I'd move farther south, but there's too much urban sprawl which makes it inconvenient at best to get around unless you drive everywhere. Mountain View is going up too thanks to Google.
The last place of refuge is pretty much Sunnyvale and San Jose. But the rent there is still a few hundred higher per month at least than it was two years ago.
I just started renting a 3BR house in the tri-valley area just east of Oakland at $3100/mo. It's a more suburban area with good schools, though, which tends to raise the price for potential families.
