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.
As an agent who lives in Elk Grove I thought I'd toss in my two cents. Personally I love the family feel of this city and I like that for a city of 150k people it does not feel like that, ie the streets do not have very heavy congestion in comparison to Watt Ave or Howe Ave during the rush hours. Elk Grove is part of Sacramento County, we do not have our own county so the taxes are the same however there are several area's of Elk Grove (new construction) that have what is called Mello-Roos, this is technically not a tax but a loan that the homeowners pay to cover the costs of laying in all the streets, new fire departments needed and such. Some areas can have high Mello-Roos, others have little to none, that is something we can check for you prior to you writting any offers on homes though.
Elk Grove has pretty low crime stats (look at crimemapping.com for true comparisions) which is my personal favorite and the reason why my husband and I moved here. Most of Natomas you would need flood insurance for because it is a pretty wide spread flood zone, you would not need this additional insurance for the majority of Elk Grove. Depending on what you need for commute it can be long if your traveling in rush hours, this is the one thing I do not like but I found that I can either take the 5 to avoid the 99 madness or I can use the back roads. Its rare that I have to go to Sacramento for shopping purposes since most of what I need is already here. We have loads of parks, great little trails all over, quite a bit of churches too if that is important for you. So as you can tell I favor Elk Grove, its a great place. I would say to really explore each city, drive around to look at the ammenities you like and compare the vibe each city has. I would also say to check out homes in both places, by driving around with a realtor you can get a good sense for each place.
If you have any other questions or would like to check out some places, give me a ring and I'll be happy to show you around.
If you currently live in the area, spend time in each area, driving, shopping, visiting ...get familiar with the areas and the choice may become clearer.
So several options to weigh, there are just a few for you.