Flash photography on young, still developing eyes can be harsh and in some cases, even damaging. It is better to wait until the flash isn't needed. However, a few thicknesses of tissue taped to the flash unit to diffuse the light is recommended if you must take facial pictures.
Most digital camera have an option of turning the flash off. Do you know how to use your camera settings? If not, look in your camera's manual for how to turn off the flash. You can also change your exposure and ISO settings (on some cameras) which will brighten up the picture. That's what I'm doing until it's safe.
Are their eyes open yet? Once their eyes are open you know they are fully developed and it's a lot safer and a lot less likely to cause damage if you're careful. The filter is a good idea, as is using a zoom.
The best, of course, would be to take them when the flash isn't needed, in daylight. And if their eyes are open, as long as Mom is okay with it, you can take them out for short times and play with them. Just be careful not to pick them up too high from the ground, they can get scared from the height. Unless necessary, you''re best off by sitting by them and doing your thing close to the ground, and to their height.