If you havn't found one yet, Panasonic industrial makes a N terminated magnetron, model TO-75. It's output is only 200 watts though, might not be suitible for your app. Good luck, I'm sure other manufacturers will have sim. products.
A company called Awi Build a 300 and 600 watt magnetron Mobel number AM744 and AM745. Its use in conjuction with a waveguide with a N type 7/16 connector.