In my mind, it depends on what your annual volume is, and how long the project is expected to last for. If the annual volume is extremely high (with small lot sizes) and is going to last for a year or two, I'd probably look at a custom machine with several stations, all based on a rotary nest design. Maybe 4 stations, 2 for drilling and 2 for tapping? As your tapping procedure will likely be your slowest procedure, your hourly throughput will be based on tapping machine throughput. And, once you have the machine dialed in, you really should only have to start it up and quickly run your 1000 parts. We have a similar machine in house that does drilling, tapping, and a broach deburr. I think that one ran us around $40K. It doesn't have the bells and whistles, but it's accurate and fuctional.
If it's not that high, the NC machine will likely be your best friend, especially if you already have one in house.