I am concerned that you say your Realtor won't help much....what do you mean by this? I am also guessing you have been preapproved by a lender to assure you a smooth loan process.
Are you choosing these areas because they are close to work or affordeabality? There are safe areas in Oakland that are affordable, ask your Realtor to show you some.
My advice is to choose a home where you and your family will feel safe. Your home choice should not be entirely driven by price, however be careful not to over buy.
How do you feel about Hayward? There are a lot of homes on the market and there are some amazing deals being negotiated there.
The big window is an easy fix...that is minor issue and not a deciding factor. You concern about safety is...ask your husband what is the dollar value of you and your kids life worth relative to a "deal" on a house.
Get a house that fits your family and lifestyle within your budget...then your house is more likely to become a home.
I don't know what you mean when you say that your Realtor won't help much. Has he/she provided you comps and helped you walk through a comparison of sold, under contract, and competitive properties?
I suspect that none of us on Trulia Voices will be able to provide you specific advice about the properties and it seems that is what you really want and need. In order for any Realtor to advise you on these, we would need to have a command of that market and an understanding of your needs and objectives. That is probably beyond the scope of what this board can provide.
That, however, does not mean the people here on Trulia won't try to help you. Perhaps we can help you get what you seek in terms of help. Mansur makes an excellent recommendation of speaking w/ your Realtor and his/her manager. If you can elaborate on what help you want, maybe be can make some suggestions for increasing the help results you are getting from your Realtor.