Go with the vaccinations, without a doubt. There is a lot of bad information being spread around out there by a very vocal minority about the risks of vaccinations. The truth is, the risks are very low, and there isn't any conclusive evidence that there is any connection between vaccinations and autism. Many of those against vaccinations point out that the first signs of autism occurred shortly after getting vaccinated. Well, it also turns out that this is just the time of life that signs of autism typically start showing up, vaccinations or not - correlation does not imply causation.
At the end of the day, the tiny risk involved with getting vaccinated is well worth it for the diseases & illnesses they are preventing.