Hello and welcome!
I can vouch for the axunworks box. It can do JAMMA, JVS, autofire buttons, button remapping, kick harness support, has a built in power supply with voltmeter, adjustable 5v and 3.3v, and it's very well made. The accessories are excellent as well, especially the JAMMA extender with voltmeter. The HAS is also very well respected though I haven't used one personally. I think either one would suit your needs very well, though if you're going to do anything JVS (like Naomi) I would go for the Axunworks box.
As for controllers, any supergun with Neo Geo ports will allow you to use the Undamned USB decoders, which will allow you to use almost any USB arcade stick/controller you want with the setup. I can personally vouch for them as well.