What's the best way to treat metatarsalgia that doesn't seem to be responding to wearin comfortable shoes and resting?

Rest isn't enough. The cause of the metatarsalgia has to be looked into. There may be something mechanical in how you are built and/or walk which needs to be addressed, possibly via the use of a custom orthotic. There can be other causes too, depending on the nature of the symptoms. I'd suggest consulting with a friendly podiatrist.
See a doctror. You need to make sure that there is not a fracture. You can try to wear an over counter orthotic to support the arch and metatarsals.
Metatarsalgia. Your next step would be to get weight bearing x-rays. Also place orthotics inside your shoes to add support and cushion.