In terms of cost I would say that some parts of San Mateo are cheaper than the other towns, but they don't look as nice, not that there is a crime problem or anything like that, they are just older and not updated. I would say near 19th St, or Delaware, and also east of 101.
If you're going to the airport you should check out the KX.
http://www.samtrans.org/pdf/Schedule...X_04-12-09.pdf (It is a one seat ride, versus 2 transfers for Caltrain + BART)
Generally speaking Belmont is a bit less expensive than San Carlos, I live in Belmont, but I live in the Carlmont Village area, near Ralston and Alameda de Las Pulgas, that would be close to the 260 bus, but I wouldn't recommend it if you're going to be using public transportation, the neighborhood is nice, and partially in the hills. The 'downtown' Belmont area has apartments near Old Country road, which are somewhat close to the Caltrain tracks. The area is not as nice in that there is industrial property right next to the track, and the neighborhood is a bit more working class, but I would say it is still pretty safe, and there is nothing wrong with it. There is also one apartment complex (with a condo complex behind it) on Davey Glen Rd. on the other side of El Camino, which is walking distance to the station, and a few apartment complexes on Ralston a bit west of El Camino. You can sometimes rent condos from the owners, though you only see one available every few months. The apartments on Old Country Rd tend to be fairly affordable relative to the peninsula. Of course you might prefer San Carlos, since that does have a real downtown along Laurel St. versus Belmont which really doesn't.
Redwood Shores and Foster City tend to be even more expensive, Redwood Shores being the most expensive, both being on the other side of 101 they are not close to Caltrain, but the neighborhoods all look nice, with a lot of lagoons in both.
If I were you I would look to live close to the San Carlos Caltrain or Belmont Caltrain since the KX stops at both of those, and of course there is Caltrain there too. One nice thing you will find in the area is that there are no at-grade intersection between Caltrain and the streets, which is nice because that means they don't blow the train horns in Belmont or San Carlos.
Some places that advertise on craigslist don't have a manager on site from 9-5 everyday, I would email or call them to set up an appointment before hand. You probably have a bit of negotiating room nowadays with the vacancy rate going up, but you'll probably find this area to be more expensive in terms of rent than Florida, and expect most apartments to have been built in the 70s. There are some newer ones but they tend to be more expensive, and mostly concentrated in Redwood Shores and Foster City.