I can recommend Eastern & Southern Safaris in Nairobi which I've used on 3 trips. They can put together a custom, private itinerary for you starting in Nairobi, going on to Ngorongoro Crater and back. In Tanzania, they use Leopard Tours as their ground operator.
In general, vehicles and guides don't cross over, so on a combined Kenya/Tanzania itinerary, you'll have different ground operators for each country but they coordinate with each other so that your transition is smooth.
What time of year are you traveling and aside from Ngorongoro, where did you want to go? Logistically, it would be easy to include Amboseli, Lake Manyara, and/or Tarangire along the way on a route between Nairobi and Ngorongoro.
Good luck with your planning!