Elk Grove has a very good school district which is important for you since you have 3 kids. Elk Grove is bigger and as a city it has its own police, etc.
Natomas has only a few (charter) schools which are good. However they are full, and not so easy to get in. Also, in Natomas you will need flood insurance. It is also close to Del Paso Heights, which is a low income, high crime neighborhood. However, on the plus side, Natomas is much more strategically located, very near the airport, very near downtown. A lot of shopping centers near by, etc.
It is a trade-off to choose between the two, and it all depends on your own circumstances. If your kids education are very important factors, probably you should be considering Elk Grove.