I can not speak with any great wisdom about each of the baseball programs.
However, you better understand the nature of the school you are attending. SFSU is an urban state university; the student body is a reflection of it's location. Remember you will be a student more than you will be a baseball player.
CSUEB was a D3 a few years ago. The transition was more about finding local competition than a change in the program (there are no D3's in NorCal). CSUEB is more of a suburban campus and as such you have a broader reach in the student body.
The comments about these schools being transfer schools is very accurate. I can not speak first hand about the programs, I would be surprised if less than 90% of there players (the ones that play) are transfer students.
Before I get too excited about either program, I would spend a day on the campus. Go to a few classes, eat in the dining common. If after a day you find this appealing, then go pro active with the baseball programs.