I have been receiving physical therapy for a year for achilles tendonitus with little improvement. An MRI taken yesterday shows deep inflammation but no tearing. The next step will be cortisone and a boot, which won't be for another few weeks. I would like to start with better shoes and perhaps some other more natural alternatives. Your thoughts?

I would recommend a shoe with an elevated heel. This will take the stress off the Achilles' tendon. A Hoka shoe is a possibility. I would also use an arch support with a deep heel cup to keep your heel from rotating.  Walking barefoot should be avoided, and we frequently recommend slipper/house-shoes made by Haflinger and sandals made by Vionic.  Both have excellent arch support and can be worn indoors and, in the case of the Vionic, in the shower to prevent having to walk barefoot.  Using a plantar fascia night splint is also good to keep the tendon elongated.